7M2V | pdb_00007m2v

Crystallographic Structure of the Rhombohedral Crystal Form of STMV Grown from Chloride

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 grown by sitting drop vapor diffusion in Cryschem plates with 0.6 ml reservoirs and 6 to 8 ul drops. Drops were equal amounts of a 5 mg/ml virus stock solution buffered at pH 6.5 with 0.1 M phosphate, and the reservoir solution. The reservoir solution was 4% w/v NaCl in 0.1 M phosphate at pH 6.0. Crystallization was at 4 degrees C.

Crystal Properties
Matthews coefficient	Solvent content
2.5	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 165.634	α = 90
b = 165.634	β = 90
c = 433.315	γ = 120

Symmetry
Space Group	H 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		2002-06-15	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	1.8	55.3	84	0.08	0.075	0.998	13.4	4.5		345430			11

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.85			0.146	0.14	0.54	2.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (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	1.8	50	345430	17134	84	0.2054	0.21	0.2168	0.22

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	22409
Nucleic Acid Atoms	4220
Solvent Atoms	5564
Heterogen Atoms	41

Software

Software
Software Name	Purpose
PHENIX	refinement
d*TREK	data reduction
Aimless	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.