4V5T | pdb_00004v5t

X-ray structure of the Grapevine Fanleaf virus

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Y26	PDB ENTRY 2Y26

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	CRYSTALS OF GFLV-F13 WERE GROWN AT 293K BY VAPOR DIFFUSION (1 MICROLITER SITTING DROPS) WITH A VIRUS SOLUTION AT 2.2 MG/ML AND A RESERVOIR CONTAINING 4% (M/V) PEG 3350, 0.1 M HEPES NA PH 7.5 AND 0.2% (M/V) AGAROSE.

Crystal Properties
Matthews coefficient	Solvent content
5.27	76.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 279.4	α = 102.4
b = 279.6	β = 116.4
c = 293.3	γ = 108.2

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2009-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA		SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	135.426	88.1	0.1	9.2	2		1214112			36.31

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.08	71.7		0.36	2.5	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	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	PDB ENTRY 2Y26	3	135.426	1214112	60925	88.26	0.1911	0.1902	0.19	0.2073	0.2	36.27

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]
0.628	-0.5939	2.5481	-5.1409	5.1099	5.5261

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.539
f_angle_d	1.195
f_chiral_restr	0.077
f_bond_d	0.01
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	79020
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
AMoRE	model building
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
AMoRE	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.