Experiment: 3VGK

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3VGM	PDB ENTRY 3VGM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.1M Tris-HCl (pH 7.5), 16% PEG 3350, 0.2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.81	67.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.69	α = 90
b = 173.7	β = 106.69
c = 124.03	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 270		2008-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.00000	Photon Factory	BL-17A

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	3.25	20	96.3	0.113	10.15			60768		-3	76.659

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.25	3.33	97.6		0.829	0.954	2.14

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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3VGM	3.25	20	60748	6121	96.85	0.2119	0.2059	0.21	0.2644	0.26	RANDOM	87.3443

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]
-0.39		-1.54	0.87		-1.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.942
r_dihedral_angle_3_deg	19.556
r_dihedral_angle_4_deg	17.879
r_dihedral_angle_1_deg	6.464
r_scangle_it	1.828
r_angle_refined_deg	1.449
r_scbond_it	1.008
r_angle_other_deg	0.919
r_mcangle_it	0.899
r_mcbond_it	0.469

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.942
r_dihedral_angle_3_deg	19.556
r_dihedral_angle_4_deg	17.879
r_dihedral_angle_1_deg	6.464
r_scangle_it	1.828
r_angle_refined_deg	1.449
r_scbond_it	1.008
r_angle_other_deg	0.919
r_mcangle_it	0.899
r_mcbond_it	0.469
r_mcbond_other	0.081
r_chiral_restr	0.073
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18124
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	18

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	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.