5BKQ | pdb_00005bkq

Crystallographic structure of a cubic form of STMV grown from nitrate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4OQ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	279	Crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs. Drops were equal amounts of a 5 mg/ml virus stock solution buffered with 0.1 M phosphate at pH 6.5, and the reservoir solution which was 20% w/v sodium nitrate in 0.1 M phosphate at pH 6.0. Crystallization was carried out at 4 degrees C.

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 234.05	α = 90
b = 234.05	β = 90
c = 234.05	γ = 90

Symmetry
Space Group	P 2 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	173	CCD	MAR CCD 165 mm		2002-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.0	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	3.18	105	0.65	0.143	0.142	0.964	11.5	3.8		45796			50.45

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.18	3.25			0.235	0.46	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4OQ8	3.19	75	1.33	45793	1923	64.22	0.2627	0.2608	0.24	0.2732	0.27	54.84

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	10.1231
f_angle_d	0.4849
f_chiral_restr	0.0467
f_plane_restr	0.0044
f_bond_d	0.0026

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	22980
Nucleic Acid Atoms
Solvent Atoms	1583
Heterogen Atoms	417

Software

Software
Software Name	Purpose
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.