Cryo-EM PDB File Format Template



EXPDTA    CRYO-ELECTRON MICROSCOPY
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : EM REFINEMENT
REMARK   3   SOFTWARE PACKAGES      : MRC SUITE, SPIDER, EMBL ICOS PACKAGE
REMARK   3   RECONSTRUCTION SCHEMA  : SPHERICAL HARMONICS
REMARK   3
REMARK   3
REMARK   3 EM MAP-MODEL FITTING AND REFINEMENT
REMARK   3   ATOMIC MODELS              : X-RAY DIFFRACTION STRUCTURES
REMARK   3   REFINEMENT SPACE           : REAL
REMARK   3   REFINEMENT PROTOCOL        : RIGID BODY REFINEMENT
REMARK   3   REFINEMENT TARGET          : R-FACTOR
REMARK   3   OVERALL ANISOTROPIC B VALUE: NULL  
REMARK   3
REMARK   3 FITTING PROCEDURE : THE CRYSTAL STRUCTURE OF THE CAPSID
REMARK   3  PROTEIN FROM CHOI ET AL (1997) PROTEINS 3 27:345-359
REMARK   3  (SUBUNIT A OF PDB FILE 1VCQ) WAS PLACED INTO THE CRYO-EM
REMARK   3  DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY POSITIONED
REMARK   3  INTO THE CRYO-EM DENSITY CORRESPONDING TO POSITIONS OF THE
REMARK   3  FOUR INDEPENDENT MONOMER DENSITIES BETWEEN THE INNER LEAFLET
REMARK   3  OF THE BILAYER AND THE RNA. THESE POSITIONS WERE THEN REFINED
REMARK   3  BY RIGID BODY REFINEMENT IN REAL SPACE WITH THE PROGRAM EMFIT
REMARK   3  (CHENG ET AL. 1995, CELL 80, 621-630).  THE QUALITY OF THE FIT
REMARK   3  CAN BE SEEN FROM THE MAP DENSITY WITHIN THE PROTEIN. ALL 4563
REMARK   3  ATOMS ARE IN DENSITY OF AT LEAST 4 SIGMA (96.73) ABOVE THE
REMARK   3  AVERAGE (512.04), 1167 ATOMS ARE IN DENSITY BETWEEN 4 AND 5
REMARK   3  SIGMA, 3174 ATOMS ARE IN DENSITY BETWEEN 5 AND 6 SIGMA, AND 222
REMARK   3  ATOMS ARE IN DENSTY OF 6 SIGMA OR ABOVE. THE VARIATION IN
REMARK   3  DENSITY OVER THE FITTED PROTEIN CAN BE VISUALIZED WITH THE
REMARK   3  PSEUDO TEMPERATURE FACTOR. THE DENSITY VALUE AT EACH ATOM IS
REMARK   3  GIVEN IN THE 8TH COLUM (USUALLY THE OCCUPANCY) AS THE NUMBER
REMARK   3  OF STANDARD DEVIATION ABOVE BACKGROUND. COLUMN NINE (USUALLY
REMARK   3  THE TEMPERATURE FACTOR) CONTAINS THE VALUE OF THE RELATIVE
REMARK   3  DENSITY WITHIN THE FITTED PROTEIN SCALED LINEARLY SO THAT THE
REMARK   3  MINIMUM DENSITY IS 100.0 AND THE MAXIMUM DENSITY IS 1.0.  THE
REMARK   3  ATOMS THAT LIE IN THE LOWER DENSITY REGIONS WILL HAVE THE
REMARK   3  HIGHEST PSEUDO TEMPERATURE FACTORS.
REMARK   3
REMARK   3
REMARK   3 EM IMAGE RECONSTRUCTION STATISTICS
REMARK   3   NOMINAL PIXEL SIZE (ANGSTROMS)    : 2.64
REMARK   3   ACTUAL PIXEL SIZE  (ANGSTROMS)    : 2.52
REMARK   3   EFFECTIVE RESOLUTION (ANGSTROMS)  : 9.0
REMARK   3   NUMBER OF PARTICLES               : 5267
REMARK   3   CTF CORRECTION METHOD             : NULL
REMARK   3
REMARK   3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: THE PIXEL SIZE
REMARK   3    OF THE CRYO-EM MAP WAS CALIBRATED AGAINST THE ATOMIC MODEL OF
REMARK   3    THE NUCLEOCAPSID. DENSITIES WERE COMPARED BY CROSS-CORRELATION
REMARK   3    WITHIN A SPHERICAL SHELL OF INTERNAL RADIUS 169 ANGSTROMS AND
REMARK   3    EXTERNAL RADIUS 198 ANGSTROMS.
REMARK   3
REMARK   3 OTHER_DETAILS: THE COORDINATES ARE IN THE P, Q, R FRAME IN
REMARK   3  ANGSTROM UNITS AND CORRESPOND TO ICOSAHEDRAL SYMMETRY AXES.
REMARK   3  THE ORIGIN IS CHOSEN AT THE CENTER OF THE VIRUS WITH P, Q
REMARK   3  AND R ALONG MUTUALLY PERPENDICULAR TWO-FOLD AXES OF THE
REMARK   3  ICOSAHEDRON. THEY SHOULD REMAIN IN THAT FRAME FOR THE EASE
REMARK   3  OF THE USER IN CREATING THE BIOLOGICALLY SIGNIFICANT VIRAL
REMARK   3  COMPLEX PARTICLE USING THE 60 ICOSAHEDRAL SYMMETRY OPERATORS
REMARK   3  RESIDUES NOT VISIBLE IN THE ORIGINAL CRYSTAL STRUCTURES ARE
REMARK   3  NOT INCLUDED IN THE CRYO-EM STRUCTURE MODEL. FOR EXAMPLE,
REMARK   3  C RESIDUES 1-118, ARE NOT VISIBLE IN THE CRYSTAL STRUCTURE
REMARK   3  (PDB ENTRY 1VCQ) AND THEREFORE ARE NOT INCLUDED IN THE
REMARK   3  COORDINATES BELOW.
REMARK   3




REMARK 245
REMARK 245 EXPERIMENTAL DETAILS
REMARK 245                          
REMARK 245   EXPERIMENT TYPE : CRYO-ELECTRON MICROSCOPY 
REMARK 245
REMARK 245
REMARK 245 ELECTRON MICROSCOPE SAMPLE
REMARK 245   SAMPLE AGGREGATION STATE       : HELICAL 
REMARK 245   NAME OF SAMPLE      	    : KINESIN DECORATED MICROTUBULE 
REMARK 245   SAMPLE CONCENTRATION (MG ML-1) : 3.5 
REMARK 245   SAMPLE SUPPORT DETAILS         : HOLEY CARBON  
REMARK 245   SAMPLE VITRIFICATION DETAILS   : PLUNGED INTO ETHANE 
REMARK 245   SAMPLE BUFFER                  : PHOSPHATE
REMARK 245   PH                             : 7.4
REMARK 245 OTHER_DETAILS: THE SAMPLE CONSISTS OF A KINESIN-DECORATED
REMARK 245  MICROTUBULE. THE EXPERIMENT DESCRIBES A MICROTUBULE-RELATED
REMARK 245  PROCESS.
REMARK 245  

REMARK 245
REMARK 245 DATA ACQUISITION
REMARK 245   DATE OF EXPERIMENT                : 15 JUNE 1998
REMARK 245   NUMBER OF MICROGRAPHS-IMAGES      : 48
REMARK 245   TEMPERATURE (KELVIN)              : 95
REMARK 245   MICROSCOPE MODEL                  : PHILIPS CM200 FEG
REMARK 245   DETECTOR TYPE                     : SO-163 FILM
REMARK 245   MINIMUM DEFOCUS (NM)              : 975
REMARK 245   MAXIMUM DEFOCUS (NM)              : 7600
REMARK 245   MINIMUM TILT ANGLE (DEGREES)      : 0
REMARK 245   MAXIMUM TILT ANGLE (DEGREES)      : 0
REMARK 245   NOMINAL CS                        : 2
REMARK 245   IMAGING MODE                      : LOW DOSE
REMARK 245   ELECTRON DOSE (ELECTRONS NM**-2)  : 1000
REMARK 245   ILLUMINATION MODE                 : BRIGHT FIELD
REMARK 245   NOMINAL MAGNIFICATION             : 50000
REMARK 245   CALIBRATED MAGNIFICATION          : 50050
REMARK 245   SOURCE                            : FIELD EMISSION GUN
REMARK 245   ACCELERATION VOLTAGE (KV)         : 200      
REMARK 245 OTHER_DETAILS: SAMPLES WERE MAINTAINED AT LIQUID NITROGEN
REMARK 245  TEMPERATURES IN THE ELECTRON MICROSCOPE.
REMARK 245  




EXAMPLE 1 

REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 THIS ENTRY CONTAINS 4 CHAIN(S). SEE REMARK 350 FOR
REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
REMARK 300                                                                  
REMARK 300 ASSEMBLY COMPONENTS
REMARK 300  COM_ID: 1;
REMARK 300   NAME:MICROTUBULE;
REMARK 300   GO_ID: 0005874;
REMARK 300   OLIGOMERIC STATE: HELICAL FILAMENTS;
REMARK 300   OTHER_DETAILS: MICROTUBULES ISOLATED AS TUBULIN FROM COW
REMARK 300  BRAIN (BOS TAURUS) AND FORMED 15:4 HELICES.
REMARK 300  THE TUBULIN PROTOFILAMENTS CONSISITING OF
REMARK 300  POLYMERISED ALTERNATING ALPHA AND BETA SUBUNITS;
REMARK 300  COM_ID: 2;
REMARK 300   NAME:KINESIN;
REMARK 300   GO_ID: 0005871;
REMARK 300   OLIGOMERIC STATE: DIMER;
REMARK 300   OTHER_DETAILS: KINESIN FROM DROSOPHILA WAS EXPRESSED IN
REMARK 300  ESCHERICIA COLI. A TRUNCATED AMINO-TERMINAL
REMARK 300  REGION (RESIDUES 1-392) EXTENDING BEYOND THE 
REMARK 300  MINIMAL MOTOR DOMAIN FORMED A HOMODIMER
REMARK 300

EXAMPLE 2

REMARK 300                                                                  
REMARK 300 BIOMOLECULE: 1                                                   
REMARK 300 THIS ENTRY CONTAINS THE UNIQUE  VIRAL REPEAT UNIT,       
REMARK 300 WHICH CONSISTS OF 5 CHAIN(S). SEE REMARK 350 FOR    
REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).            
REMARK 300
REMARK 300 ASSEMBLY COMPONENTS
REMARK 300  COM_ID: 1;
REMARK 300   NAME:FAB;
REMARK 300   IPR_ID: NULL;
REMARK 300   GO_ID: NULL;
REMARK 300   OLIGOMERIC STATE: DIMER;
REMARK 300   OTHER_DETAILS: ANTIBODY FRAGMENT;
REMARK 300  COM_ID: 2;
REMARK 300   NAME:VIRUS;
REMARK 300   IPR_ID: NULL;
REMARK 300   GO_ID: NULL;
REMARK 300   OLIGOMERIC STATE:NULL;
REMARK 300   OTHER_DETAILS: NULL
REMARK 300
REMARK 300 VIRUS PARTICULARS
REMARK 300  COM_ID: 2;
REMARK 300   VIRUS_HOST_CATEGORY:  VERTEBRATES ;
REMARK 300   VIRUS_HOST_SPECIES: GALLUS GALLUS ;
REMARK 300   VIRUS_HOST_GROWTH_CELL: GIZZARD ;
REMARK 300   VIRUS_TYPE: VIRUS; 
REMARK 300   VIRUS_ISOLATE: SPECIES ;
REMARK 300   ICTVDB_ID: 1.0.2.0.001
REMARK 300