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