Data items in the EM_2D_CRYSTAL_ENTITY category record the details of a 2D crystal assembly component. Space-group number from International Tables for Crystallography, Vol. A (1987). Unit-cell angle alpha in degrees of the reported structure. Unit-cell angle beta in degrees of the reported structure. Unit-cell angle gamma in degrees of the reported structure. The cell settings for this space-group symmetry. A description of special aspects of the cell choice, noting possible alternative settings. pseudo-orthorhombic standard setting from 45 deg rotation around c Unit-cell length a corresponding to the structure reported. Unit-cell length b corresponding to the structure reported. Unit-cell length c corresponding to the structure reported. The planar orientation of the 2D crystal in the 3D crystal. Hermann-Mauguin space-group symbol. Note that the H-M symbol does not necessarily contain complete information about the symmetry and the space-group origin. If used always supply the FULL symbol from International Tables for Crystallography, Vol. A (1987) and indicate the origin and the setting if it is not implicit. P 1 21/m 1 P 2/n 2/n 2/n (origin at -1) R -3 2/m The thickness of the crystal sample in the out-of-plane direction. The value of attribute id in category em_2d_crystal_entity must uniquely identify a set of the crystal parameters for this assembly component. The value of attribute entity_assembly_id in category em_2d_crystal_entity identifies a particular assembly component. This data item is a pointer to attribute id in category em_entity_assembly in the EM_ENTITY_ASSEMBLY category. Data items in the 3D_FITTING category record details of the method of fitting atomic coordinates from a PDB file into a 3d-em volume map file Example 1 - EMDB entry EM1078 <mmcif_iims:em_3d_fittingCategory> <mmcif_iims:em_3d_fitting id="1" entry_id="EM1078"> <mmcif_iims:method>AUTOMATIC</mmcif_iims:method> <mmcif_iims:ref_space>REAL</mmcif_iims:ref_space> <mmcif_iims:ref_protocol>RIGID BODY REFINEMENT</mmcif_iims:ref_protocol> </mmcif_iims:em_3d_fitting> <mmcif_iims:em_3d_fitting id="2" entry_id="EM1078"> <mmcif_iims:method>AUTOMATIC</mmcif_iims:method> <mmcif_iims:ref_space>REAL</mmcif_iims:ref_space> <mmcif_iims:ref_protocol>RIGID BODY REFINEMENT</mmcif_iims:ref_protocol> </mmcif_iims:em_3d_fitting> <mmcif_iims:em_3d_fitting id="3" entry_id="EM1078"> <mmcif_iims:method>AUTOMATIC</mmcif_iims:method> <mmcif_iims:ref_space>REAL</mmcif_iims:ref_space> <mmcif_iims:ref_protocol>RIGID BODY REFINEMENT</mmcif_iims:ref_protocol> </mmcif_iims:em_3d_fitting> </mmcif_iims:em_3d_fittingCategory> Example 2 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_3d_fittingCategory> <mmcif_iims:em_3d_fitting id="1" entry_id="1DYL"> <mmcif_iims:method>AUTOMATIC</mmcif_iims:method> <mmcif_iims:target_criteria>R-FACTOR</mmcif_iims:target_criteria> <mmcif_iims:ref_space>REAL</mmcif_iims:ref_space> <mmcif_iims:ref_protocol>RIGID BODY REFINEMENT</mmcif_iims:ref_protocol> <mmcif_iims:details> THE CRYSTAL STRUCTURE OF THE CAPSID PROTEIN FROM CHOI ET AL (1997) PROTEINS 3 27:345-359 (SUBUNIT A OF PDB FILE 1VCQ) WAS PLACED INTO THE CRYO-EM DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY POSITIONED INTO THE CRYO-EM DENSITY CORRESPONDING TO POSITIONS OF THE FOUR INDEPENDENT MONOMER DENSITIES BETWEEN THE INNER LEAFLET OF THE BILAYER AND THE RNA. THESE POSITIONS WERE THEN REFINED BY RIGID BODY REFINEMENT IN REAL SPACE WITH THE PROGRAM EMFIT (CHENG ET AL. 1995, CELL 80, 621-630). THE QUALITY OF THE FIT CAN BE SEEN FROM THE MAP DENSITY WITHIN THE PROTEIN. ALL 4563 ATOMS ARE IN DENSITY OF AT LEAST 4 SIGMA (96.73) ABOVE THE AVERAGE (512.04), 1167 ATOMS ARE IN DENSITY BETWEEN 4 AND 5 SIGMA, 3174 ATOMS ARE IN DENSITY BETWEEN 5 AND 6 SIGMA, AND 222 ATOMS ARE IN DENSTY OF 6 SIGMA OR ABOVE. THE VARIATION IN DENSITY OVER THE FITTED PROTEIN CAN BE VISUALIZED WITH THE PSEUDO TEMPERATURE FACTOR. THE DENSITY VALUE AT EACH ATOM IS GIVEN IN THE 8TH COLUM (USUALLY THE OCCUPANCY) AS THE NUMBER OF STANDARD DEVIATION ABOVE BACKGROUND. COLUMN NINE (USUALLY THE TEMPERATURE FACTOR) CONTAINS THE VALUE OF THE RELATIVE DENSITY WITHIN THE FITTED PROTEIN SCALED LINEARLY SO THAT THE MINIMUM DENSITY IS 100.0 AND THE MAXIMUM DENSITY IS 1.0. THE ATOMS THAT LIE IN THE LOWER DENSITY REGIONS WILL HAVE THE HIGHEST PSEUDO TEMPERATURE FACTORS. </mmcif_iims:details> </mmcif_iims:em_3d_fitting> </mmcif_iims:em_3d_fittingCategory> Any additional details regarding fitting of atomic coordinates into the 3d-em volume. partial Description of local variance of fit of the atomic coordinates into the 3dem volume map. The method used to fit atomic coordinates into the 3dem reconstructed map. The overall B (temperature factor) value for the 3d-em volume. Description of the quality of fit of the atomic coordinates into the 3dem volume map. The quality of fit of the atomic coordinates into the 3dem volume map. The type of protocol used in the refinement. rigid body A flag to indicate whether fitting was carried out in real or reciprocal refinement space. The quality of fit of the atomic coordinates into the 3dem volume map. best visual fit using the program O The value of attribute id in category em_3d_fitting must uniquely identify a fitting procedure of atomic coordinates into 3dem reconstructed volume map. This data item is a pointer to _entry_id in the ENTRY category. Data items in the 3D_FITTING_LIST category lists the methods of fitting atomic coordinates from a PDB file into a 3d-em volume map file Example 1 - based on EM entry 1078 The end sequence ID for the pdb entry chain used in the fitting The EM entry id pointer The chain id for the resulting fitted coordinates The PDB code for the entry produced by the fitting. Description of a particular component pdb entry used in fitting. The chain id for the entry used in fitting. The PDB code for the entry used in fitting. The symmetry required to be applied to the starting PDB entry chain before starting the fitting procedure The start sequence ID for the pdb entry chain used in the fitting The (1,1) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (1,2) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (1,3) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (1,4) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (2,1) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (2,2) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (2,3) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (2,4) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (3,1) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (3,2) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (3,3) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (3,4) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (4,1) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (4,2) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (4,3) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (4,4) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement This data item is a unique identifier. The value of attribute 3d_fitting_id in category em_3d_fitting_list is a pointer to attribute id in category em_3d_fitting in the 3d_fitting category Data items in the EM_3D_RECONSTRUCTION category record details of the 3D reconstruction procedure from 2D projections. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_3d_reconstructionCategory> <mmcif_iims:em_3d_reconstruction entry_id="1DYL" id="1"> <mmcif_iims:citation_id>1</mmcif_iims:citation_id> <mmcif_iims:resolution>9.</mmcif_iims:resolution> </mmcif_iims:em_3d_reconstruction> </mmcif_iims:em_3d_reconstructionCategory> The Amplitude correction method. Frequency amplitude correction with X-ray scattering data enhances the Fourier amplitudes of a reconstructed cryo-EM volume so they more closely resemble those of experimental low-angle X-ray scattering data. Normal amplitude correction (in which case the SNR weighted averaging of particles will still occur properly) may be applied or without it, in which case the (phase-flipped) data is not corrected during averaging, then the final 3D model is 'fixed'. This data item is a pointer to attribute id in category citation in the CITATION category. The CTF-correction method. The Contrast Transfer Function CTF compensation for low contrast specimens (e.g. frozen-hydrated), for which phase contrast is the only significant mechanism, then higher defocus levels must be used to achieve any significant transfer, and several images at different focus levels must be combined to complete the information lost from the transfer gaps of any one image. The CTF correction can be applied to each extracted particle separately or to the whole micrograph after digitisation. The simplest level of compensation is to reverse phases at the negative lobes of the CTF. CTF correction of each particle General details on the 3d recontruction Orientation determination using the random-conical data collection method. This method uses a defined geometry in the data collection, and is able to find the handedness of the structure unambiguously. Each specimen field is imaged twice, once tilted, once untilted. Particles are selected simultaneously from both untilted- and tilted-specimen fields, using a special interactive particle-selection program that is able to "predict" the location of a particle in the tilted-specimen field when its counterpart has been selected in the untilted field. From the untilted-specimen particle data set, all particles are selected that exhibit the same view. This can be done by using alignment followed by classification. The corresponding tilted-specimen data subset can be used to compute a reconstruction: the orientations of the tilted-particle projections lie on a cone with fixed angle (the tilt angle) and random azimuths (the in-plane angles found in the alignment of the untilted particle set). 1 Orientation determination using common lines (a.k.a. "angular reconstitution"). This method is based on the fact that in Fourier space any two projections intersect along a central line ("the common line"). Hence, in principle, the relative orientations between three projections can be determined - except that the handedness of the constellation is ambiguous. Because of the low signal-to-noise ratio of raw particle images, averages of projections falling into roughly the same orientation must be used. Since the procedure leads to solutions presenting local minima, it must be repeated several times to find solutions that form a cluster, presumably around the global minimum. Such clustering of solutions can be detected by multivariate statistical analysis of the resulting 3D maps. Two clusters are expected, one for each enantiomorph. After initial structure is obtained, it should be further refined using 3D projection matching strategy described next. 2 Orientation determination by 3D projection matching. Here the existing 3D map is projected in many orientations on a regular angular grid, and the resulting projections that are compared, one by one, with each of the experimental projections. This comparison (by cross-correlation ) yields a refined set of Eulerian angles , with which a refined reconstruction can be computed using one of the possible reconstruction techniques. This procedure requires iteration until the angles for each projection stabilize. 3 General details describing any local symmetry used in the single particle reconstruction The algorithm method used for the 3d-reconstruction. e.g. Random-conical reconstruction: a method of data collection and reconstruction used for single particles, typically used initially in a project, to obtain a first low-resolution reconstruction of the macromolecule [Radermacher et al., 1987]. Two images of the same specimen field are collected, one with untilted grid, the other with the grid tilted by 50 to 60 degrees. Any set of particles presenting the same view in the untilted-specimen image form a random-conical projection set in the associated tilted-specimen image. Helical reconstruction Helical reconstruction is used when the protein of interest forms a natural helix. Since the helix is a recurring structure with a very well defined pattern, the repeating pattern of the helix can be exploited to solve the structure. In this case, no alignment of the particles is needed, since the individual positions of subunits within the helix are clearly defined by the shape of the helix. Two common examples of structures solved by helical reconstruction are TMV and microtubules. Icosahedral reconstruction Icosahedral reconstructions also take advantage of internal symmetry and repetition to generate a detailed three-dimensional structure from the data set. In this case, the symmetry is icosahedral (twenty-one sided). Many viruses exhibit icosahedral symmetry in their capsid proteins, and this method has been used to solve their structures. Electron crystallography Electron crystallography is similar to x-ray crystallography in that it exploits the repeating pattern found within a crystal to generate a structure. Just as with x-ray crystallography, difraction patterns are generated and are used to define an electron density map. However, it differs in that the crystal used is a two-dimensional sheet as opposed to three three-dimensional crystals of x-ray crystallography. Common Lines Another reconstruction method searches for the intersection of any two projections in Fourier space. The Fourier transform of the experimental projections all form slices around a common core in Fourier space. Therefore, the intersection of these projections are unique (unless the projections perfectly overlap), and their relative orientation can be found when three or more projections are used. A principal problem with this method is that the handedness of the image is lost. This, however, can later be corrected by visual examination of the model with other known structural information. Back Projection As its name implies, back projection is the inverse function of projection. When an n-dimensional object is projected, each projection is an n-1 dimensional sum of its density along the projection axis. Therefore, a sphere would have circles as its projections. A cube, on the other hand, would produce either squares, diamonds, or other intermediate parallelograms depending on the direction of projection. The actual shape, of course, depends on the orientation from which the projection was made. The reverse function is called back projection and regenerates the original object. cross-common lines The number of asymmetric units used in the single particle reconstruction The number of particles used in the 3d reconstruction The final resolution (in angstroms)of the 3d reconstruction. The method used to determine the final resolution of the 3d reconstruction. The Fourier Shell Correlation criterion as a measure of resolution is based on the concept of splitting the (2D) data set into two halves; averaging each and comparing them using the Fourier Ring Correlation (FRC) technique. FSC at 0.5 cut-off The actual pixel size of projection set of images in x IF only attribute voxel_size_x in category em_3d_reconstruction is given then a cube is assumed. The actual pixel size of projection set of images in y IF only attribute voxel_size_x in category em_3d_reconstruction is given then a cube is assumed. The actual pixel size of projection set of images in z IF only attribute voxel_size_x in category em_3d_reconstruction is given then a cube is assumed. This data item is a pointer to attribute id in category entry in the ENTRY category. The value of attribute id in category em_3d_reconstruction must uniquely identify the 3d reconstruction. Data items in the EM_3D_REFINEMENT category record details about the class/particle refinement. In random conical tilt, images were assigned angular positions through rotational alignment and tilt-angles. From each different class, a three-dimensional preliminary model is constructed. To improve the output, those preliminary models from each class that have a high degree of similarity are merged. In theory, these models corresponded to groups of the same molecule just viewed from different orientations. Once all the good random conical tilt models (and their corresponding particle data sets) have been merged, iterative angular refinement is used to improve the model's resolution. Equidistant projections are first generated from the merged model. The entire particle data set (whether the old random conical tilt experimental particles, or new untilted experimental particles, or both) is then cross correlated to each reference projection. A correlation coefficient is generated between each experimental particle and reference projection. For each individual experimental particle, it is matched to the reference projection that gave the highest correlation coefficient. Therefore, it is assumed that this particle matches the Euler angles of the reference projection. Alignment radius (pixels) used in alignment search the angular_search_step_size used in refinement Convergence criterion fraction e.g. Converges when x16 % of all images move < 1.5 * stepsize This data item is a pointer to attribute id in category entry in the ENTRY category. the max_spatial_frequency used in refinement (1/A) Description of the 3d refinement method the number of iterations used in refinement The number of particles used in refinement. the Projection radius in pixels the structure_radius in pixels The value of attribute id in category em_3d_refinement must uniquely identify the refinement used in the em experiments. Data items in the EM_ARRAY_FORMATION category record details of growth conditions for the array samples. Example 1 - based on PDB entry 1AT9 and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_array_formationCategory> <mmcif_iims:em_array_formation id="1" type="2D-CRYSTAL"> <mmcif_iims:atmosphere>room air</mmcif_iims:atmosphere> <mmcif_iims:pH>5.2</mmcif_iims:pH> <mmcif_iims:temp>18.</mmcif_iims:temp> <mmcif_iims:buffer_id>2</mmcif_iims:buffer_id> <mmcif_iims:details>on grid</mmcif_iims:details> <mmcif_iims:citation_id>2</mmcif_iims:citation_id> </mmcif_iims:em_array_formation> </mmcif_iims:em_array_formationCategory> The type of the apparatus used for growing the array. Langmuir trough The type of atmosphere in which arrays were grown. room air This data item is a pointer to attribute id in category em_solution_composition. This data item is a pointer to attribute id in category citation in the CITATION category. Any additional items concerning array growth. Two-dimensional Crystallization-- Purified protein (2 mg/ml) was mixed with E. coli lipids solubilized in OTG (mixed micelles stock solution, 4 mg/ml E. coli lipids in 20 mM Mes-NaOH (pH 6), 5% OTG, 0.01% NaN3) to achieve a lipid to protein ratio of 1 (w/w). The final protein concentration was adjusted to 1.33 mg/ml, and the final OTG content was adjusted to 1.93%. The reconstitution mixture (60 µl) was preincubated at room temperature for 30 min and dialyzed against 1.5 liters of 10 mM Mes-NaOH (pH 6), 100 mM NaCl, 100 mM MgCl2, 2 mM dithiothreitol, 0.01% NaN3 for 24 h at room temperature, 24 h at 37 °C, and another 24 h at room temperature. The method used for growing the array. lipid monolayer the pH value used for growing the array. 4.7 This data item is a pointer to attribute id in category em_solution_composition in the EM_SOLUTION_COMPOSITION category. The value of the temperature in degrees Kelvin used for growing the arrays. 293 The length of time required to grow the array. approximately 2 days The value of attribute id in category em_array_formation must uniquely identify the sample. The value of attribute type in category em_array_formation must identifies the type of array studied. Data items in the EM_ASSEMBLY category record details about the type of complex assembly that describes the nature of the sample studied. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_assemblyCategory> <mmcif_iims:em_assembly id="1" entry_id="1DYL"> <mmcif_iims:name>virus</mmcif_iims:name> <mmcif_iims:aggregation_state>icosahedral</mmcif_iims:aggregation_state> <mmcif_iims:composition>virus</mmcif_iims:composition> <mmcif_iims:num_components>1</mmcif_iims:num_components> </mmcif_iims:em_assembly> </mmcif_iims:em_assemblyCategory> A description of the aggregation state of the assembly. The known composition of the assembly. A description of any additional details describing the observed sample. This structure was preferentially oriented (end-on)on the grid. 1 The structure was monodisperse. 2 The name of the assembly of observed complexes. The number of components of the biological assembly. The author determined highest resolution of the reconstruction The author determined lowest resolution of the reconstruction The author determined resolution of the reconstruction The value of attribute id in category em_assembly must uniquely identify the observed assembly. An assembly may consist of a collection of complexes. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the EM_CLASSES category record details about the particle classification. Particle classification involves grouping images that are similar, and separating images that are distinct. In practical use, this means that experimental projections that have the same orientation (shape) are placed within the same category for later averaging. In this case, orientation means that the particles are showing the same face to the viewer and the only difference between them is that they can be rotated by some angle in the plane of the image. The experimental projections might also be shifted relative to each other, but the centering of the experimental projections is often done before classification. is this required? E(e1,e2,e3) = E(w,h,i) cos(i)cos(h)cos(w)-sin(i)sin(h) cos(i)cos(h)sin(w)+sin(i)sin(h) -cos(i)sin(h) -sin(i)cos(h)cos(w)-cos(i)sin(h) sin(i)cos(h)sin(w)+cos(i)sin(h) sin(i)sin(h) sin(h)cos(w) sin(h)sin(w) cos(h) The alignment_method used The percentage angular error threshold The average_angular_error in degrees The average_translational_pixel_shift_error The clustering_method used Description of the classes derived in the em experiments. We have used size variation analyses to classify images recorded from preparations of the WT S. cerevisiae PDC to which sufficient E1 was added to occupy its 60 binding sites and the same preparation with about one-third of the E1 binding sites occupied. Two 3D reconstructions representative of images that vary in size by 10-12% (~50 Ĺ in diameter) from these preparations were computed to document the E1 organization about the core and the length of its inner linkers. In this regard, our previous structure of the WT bovine kidney PDC in which ~22 E1s were bound indicated that the outer shell could readily accommodate 60 molecules of E1 without significant crowding. Surprisingly, this study shows that extensive E1 binding favors a more extended inner linker and an altered arrangement of E1 about the core. 1 The focal pair method of orientation determination, refinement, and 3D reconstruction as implemented in the IMIRS software package was used except that an additional step of particle-size evaluation was performed in the current reconstruction. Data sets consisting of 1,500 and 690 particle images of PDC with a molar ratio of 60 E1/E2 core and ~24 E1/E2 core, respectively, were processed. For both data sets, an iterative procedure was implemented to classify the particles according to their sizes by using the SIZEDIFF program with contrast transfer function correction incorporated. A preliminary 3D reconstruction was calculated by combining all of the particles, and this "average" reconstruction was used to classify the images into a 1.0 size group comprising a 3% size variation of the images. For the PDC with ~60 E1/E2 core, the converged structure from 128 images in the 1.0 size group, was then used as a model to classify 45 and 80 images in the 0.95 and 1.05 size groups, respectively. For the WT PDC preparation (24 E1/E2 core) the converged structure from 80 images in the 1.0 size group was used as model to classify 46 and 53 images in the 0.95 and 1.05 size groups, respectively. The image size distribution appears bell-shaped and is consistent with a more extensive data set of the human PDC (Y.G., Z.H.Z., Y. Hiromasa, H. Bao, X. Yan, T. E. Roche, and J.K.S., unpublished results). The finding that 1.0 size groups consist of the larger and smaller reconstructions in the PDC preparations according to their greater or lesser degree of E1 occupancy, respectively, indicates that the extent of E1 binding is related to the variable size of the molecules. 2 A classification was performed using the self-organizing map (SOM) algorithms of the XMIPP package. The entire set was first low pass-filtered to 3.2 nm, and a reference-free alignment was performed using the Spider software package. Transformations in x, y, and in-plane angle were imposed, and the data set was fed to the kernel density SOM procedure using a 10 x 10 grid. The procedure generates a grid of code vectors that represent the assigned images. It was verified that clean looking code vectors represented classes of clean particles, while particles assigned to defect-ridden code vectors were themselves of poor quality. The procedure was repeated several times with different parameters, and in each case a set of roughly 3000 good particles was obtained. Further processing was conducted on a set containing 2943 particles. 3 The picked particles were submitted to a multivariate statistical analysis without alignment and were classified into clusters of particles with similar features. To this end, a program package kindly provided by J. P. Bretaudičre was used. The various cluster averages revealed square and round shaped particles at different angular orientations. These averages were taken as references for subsequent angular and translational alignment of the extracted 4096 particles. Aligned particles were classified again, and cluster averages were calculated. 4 This data item is a pointer to attribute id in category entry in the ENTRY category. The euler angle about z-axis The euler angle about y-axis The second euler angle about z-axis The fractional_minimum_amplitude The global_correlation_coefficient The global_real-space_correlation_coefficient flag for method used for internal resolution The number of particles used in the class average The class origin in X The class origin in Y The value of attribute id in category em_classes must uniquely identify the classes used in the em experiments. Data items in the EM_CRYO_STAIN category record details about the staining techniques used. Text describing a reference citation on the staining techniques used A mandatory flag to indicate if the data items describe cryo staining or not If the details given are for a cryogen staining method the name of the cryogen used General details on the staining techniques used The humidity at which the staining technique was used Details on the instrument used in the staining technique used Text describing the protocol for the staining techniques used A pointer to attribute id in category em_sample_preparation in the EM_SAMPLE_PREPARATION category The staining technique temperature used Text giving details on the time factors involved in the staining techniques used The general class or type of the staining technique used The value of attribute id in category em_cryo_stain must uniquely identify set of stain parameters This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the EM_DETECTOR category record details of the image detector type. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_detectorCategory> <mmcif_iims:em_detector entry_id="1DYL" id="1"> <mmcif_iims:type>KODAK SO163 FILM</mmcif_iims:type> </mmcif_iims:em_detector> </mmcif_iims:em_detectorCategory> The detector binning in x The detector binning in y Any additional information about the detection system. The detector dimension in x The detector dimension in y The exposure time in micro-seconds The exposure type Description of film_processing_conditions The detector offset in x from the top left corner of the CCD The detector offset in y from the top left corner of the CCD This data item is a pointer to attribute id in category entry in the ENTRY category. The detector pixel size The detector read-out speed The detector type used for recording images. Usually film or CCD camera. This data item is a pointer to attribute id in category entry in the ENTRY category. The value of attribute id in category em_detector must uniquely identify the detector used for imaging. Data items in the EM_ELECTRON_DIFFRACTION category record details about the electron diffraction data from the electron crystallography experiment. Example 1 - based on PDB entry 1TUB and laboratory records for the structure corresponding to PDB entry 1TUB <mmcif_iims:em_electron_diffractionCategory> <mmcif_iims:em_electron_diffraction entry_id="1TUB" id="1"> <mmcif_iims:num_structure_factors>12000</mmcif_iims:num_structure_factors> <mmcif_iims:details xsi:nil="true" /> </mmcif_iims:em_electron_diffraction> </mmcif_iims:em_electron_diffractionCategory> Details of the electron diffraction experiment THE MODEL WAS DERIVED USING ELECTRON DIFFRACTION AND IMAGE DATA FROM TWO DIMENSIONAL CRYSTALS OF TUBULIN INDUCED BY THE PRESENCE OF ZN++ IONS. WHAT FOLLOWS ARE THE COORDINATES FOR THE AB-TUBULIN DIMER BOUND TO TAXOL AS OBTAINED BY ELECTRON CRYSTALLOGRAPHY OF ZINC-INDUCED SHEETS. THIS IS THE UNREFINED MODEL, BUILT INTO A RAW DENSITY MAP WHERE THE RESOLUTION IN THE PLANE OF THE SHEET WAS 3.7 ANGSTROMS AND THAT PERPENDICULAR TO THE SHEET ABOUT 4.8 ANGSTROMS. THE MODEL DOES NOT CONTAIN MOST OF THE C-TERMINAL RESIDUES OF EITHER MONOMER WHICH WERE DISORDERED IN THE MAP. THE LOOP BETWEEN HELIX H1 AND STRAND S2, AND THAT BETWEEN H2 AND S3 ARE PRESENT FOR COMPLETENESS BUT WERE BUILT INTO VERY WEAK DENSITY. GIVEN THE LIMITED RESOLUTION OF THE MAP, THE CONFORMATION OF THE SIDE CHAINS, ESPECIALLY THOSE CORRESPONDING TO RESIDUES ON THE SURFACE OF THE DIMER, MUST BE TAKEN CAUTIOUSLY. IN ADDITION, BECAUSE THIS IS AN UNREFINED MODEL, CERTAIN GEOMETRY ERRORS MAY STILL BE PRESENT IN THE STRUCTURE. PLEASE TAKE THIS INTO ACCOUNT WHEN INTERPRETING YOUR OWN DATA BASED ON THE PRESENT TUBULIN STRUCTURE. ALTHOUGH THE POSITION OF RESIDUES (WITH THE EXCEPTION OF THOSE IN THE LOOPS MENTIONED ABOVE) SHOULD NOT CHANGE SIGNIFICANTLY UPON REFINEMENT, DRAWING INFORMATION AT THE LEVEL OF SIDE CHAIN CONFORMATION IS CLEARLY NOT ADVISED. FINALLY, PLEASE NOTICE THAT THE TAXOID IN THE MODEL IS THE TAXOL DERIVATIVE TAXOTERE. 1 The number of diffraction patterns used from the electron diffraction experiment. The number of structure factors from the electron diffraction experiment. 12000 The value of attribute id in category electron_diffraction must uniquely identify the electron diffraction experiment. This data item is a pointer to attribute id in category entry in the ENTRY category. data items in the em_electron_diffraction_pattern category record details about the pattern information from the electron diffraction experiment. example 1 - based on pdb entry 1tub and laboratory records for the structure corresponding to pdb entry 1tub <mmcif_iims:em_electron_diffraction_patternCategory> <mmcif_iims:em_electron_diffraction_pattern entry_id="1TUB" id="1"> <mmcif_iims:num_patterns_by_tilt_angle>1</mmcif_iims:num_patterns_by_tilt_angle> <mmcif_iims:num_images_by_tilt_angle>4</mmcif_iims:num_images_by_tilt_angle> </mmcif_iims:em_electron_diffraction_pattern> </mmcif_iims:em_electron_diffraction_patternCategory> the number of images by tilt angle. 4 the number of diffraction patterns by tilt angle. 1 the tilt angle at which the diffraction pattern was obtained. the value of attribute id in category electron_diffraction_pattern must uniquely identify the electron diffraction pattern experiment. this data item is a pointer to attribute id in category entry in the ENTRY category. data items in the em_electron_diffraction_phase category record details about the phase information from the electron diffraction experiment. example 1 - based on pdb entry 1tub and laboratory records for the structure corresponding to pdb entry 1tub <mmcif_iims:em_electron_diffraction_phaseCategory> <mmcif_iims:em_electron_diffraction_phase entry_id="1TUB" id="1"> <mmcif_iims:d_res_high>4.0</mmcif_iims:d_res_high> </mmcif_iims:em_electron_diffraction_phase> </mmcif_iims:em_electron_diffraction_phaseCategory> the highest resolution d-value for the electron diffraction experiment. 5.0 the highest resolution shell error in degrees. the overall phase error in degrees. the rejection criteria (phase error) in degrees. the phase residual value for the electron diffraction experiment. the value of attribute id in category electron_diffraction_phase must uniquely identify the electron diffraction phase experiment. this data item is a pointer to attribute id in category entry in the entry category. Data items in the EM_EMBEDDING_AGENT category record details about the type of reagents into which the sample was embedded Details on a reference citation on the embedding agent used General details on the embedding agent used The temperature the embedding agent was used at Details about the effect of time resolution for the embedding agent used The type of embedding agent used The value of attribute id in category em_embedding_agent must uniquely identify set of the embedding agent parameters This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the EM_ENTITY_ASSEMBLY category record details about each component of the assembly or complex. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_entity_assemblyCategory> <mmcif_iims:em_entity_assembly id="1" assembly_id="1"> <mmcif_iims:type>VIRUS</mmcif_iims:type> </mmcif_iims:em_entity_assembly> </mmcif_iims:em_entity_assemblyCategory> Additional details about the component. The Gene Ontology (GO) identifier for the component. The GO id is the appropriate identifier used by the Gene Ontology Consortium. Reference: Nature Genetics vol 25:25-29 (2000). GO:0005876 GO:0015630 The InterPro (IPR) identifier for the component. The IPR id is the appropriate identifier used by the Interpro Resource. Reference: Nucleic Acid Research vol 29(1):37-40(2001). 001304 002353 The name of the component of the observed assembly. The cell from which the component was obtained. CHO HELA 3T3 The cellular location of the component. cytoplasm endoplasmic reticulum plasma membrane A flag to indicate whether the component is engineered. The expression system used to produce the component. eschericia coli saccharomyces cerevisiae The plasmid used in the expression system used to produce the component. pBR322 pMB9 The organelle from which the component was obtained. golgi mitochondrion cytoskeleton The common name of the species of the natural organism from which the component was obtained. The species of the natural organism from which the component was obtained. The strain of the natural organism from which the component was obtained, if relevant. DH5a BMH 71-18 The tissue of the natural organism from which the component was obtained. heart liver eye lens Alternative name of the component. FADV-1 A description of the biological structure type of the assembly component. The value of attribute id in category em_entity_assembly must uniquely identify each of the components of the assembly or complex. The value of attribute assembly_id in category em_entity_assembly identifies the assembly or complex to be described. This data item is a pointer to attribute id in category em_assembly in the EM_ASSEMBLY category. Data items in the EM_ENTITY_ASSEMBLY_LIST category record details of the structural elements in each assembly component. Example 1 - microtubule <mmcif_iims:em_entity_assembly_listCategory> <mmcif_iims:em_entity_assembly_list entity_assembly_id="1" id="1" entity_id="1"> <mmcif_iims:details>DIMER</mmcif_iims:details> <mmcif_iims:number_of_copies>2</mmcif_iims:number_of_copies> </mmcif_iims:em_entity_assembly_list> </mmcif_iims:em_entity_assembly_listCategory> The oligomeric state of the entity. The value (in megadaltons) of the molecular weight of each component of the assembly determined by attribute mol_wt_method in category em_entity_assembly_list. The method used in determining the molecular weight. Scanning Transmission Electron Microscopy Mass Measurement-- PM28 isoforms solubilized in OTG were adsorbed for 1 min to glow discharged thin carbon films supported by a thick fenestrated carbon layer (directly after cation-exchange chromatography). The gold-plated copper grids were then washed on 8 drops of quartz double-distilled water and were freeze-dried at -80 °C overnight in the microscope. For mass analysis, annular dark-field images were recorded in a STEM (VG-HB5) at 80 kV and doses of 325 ± 35 electrons/nm2. Digital acquisition of the images and microscope parameters, system calibration, and mass analysis were carried out as described previously. The total experimental error was calculated as the standard error of the mean, plus 5% of the measured particle mass to account for the absolute calibration uncertainty. The number of copies of the entity. This data item is a pointer to attribute id in category em_entity_assembly in the ENTITY_ASSEMBLY category. The value of attribute id in category em_entity_assembly_list must uniquely identify the component. A pointer to entity id. Data items in the EM_ENTITY_ASSEMBLY_MOL_WT category record details of the molecular weight of structural elements in each component. Example 1 - microtubule <mmcif_iims:em_entity_assembly_mol_wtCategory> <mmcif_iims:em_entity_assembly_mol_wt id="1" entity_assembly_list_id="1"> <mmcif_iims:mol_wt>12000.</mmcif_iims:mol_wt> <mmcif_iims:mol_wt_method>Calculated</mmcif_iims:mol_wt_method> </mmcif_iims:em_entity_assembly_mol_wt> </mmcif_iims:em_entity_assembly_mol_wtCategory> The value (in megadaltons) of the experimentally determined molecular weight of each component of the assembly. The method used in determining the molecular weight. Scanning Transmission Electron Microscopy Mass Measurement-- PM28 isoforms solubilized in OTG were adsorbed for 1 min to glow discharged thin carbon films supported by a thick fenestrated carbon layer (directly after cation-exchange chromatography). The gold-plated copper grids were then washed on 8 drops of quartz double-distilled water and were freeze-dried at -80 °C overnight in the microscope. For mass analysis, annular dark-field images were recorded in a STEM (VG-HB5) at 80 kV and doses of 325 ± 35 electrons/nm2. Digital acquisition of the images and microscope parameters, system calibration, and mass analysis were carried out as described previously. The total experimental error was calculated as the standard error of the mean, plus 5% of the measured particle mass to account for the absolute calibration uncertainty. The value of attribute id in