Experiment: 3VKS

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3B0G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	277	PEG4000, Tris-HCl, MgCl2, MPD, NaNO2, ascorbic acid, pH 8.5, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.758	α = 90
b = 132.758	β = 90
c = 77.539	γ = 90

Symmetry
Space Group	P 4 21 2

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	Bruker DIP-6040	Horizontal focusing mirror	2008-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.4	50	99.6	0.062	0.062	9	9.1	134875	134875			21.9

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	1.4	1.45	100		0.499	3.58	8.7	13352

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	3B0G	1.4	23.49	134823	134823	6771	100	0.1617	0.1617	0.1613	0.16	0.1678	0.17	RANDOM	18.0772

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]
-0.1			-0.1		0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.781
r_dihedral_angle_4_deg	12.715
r_dihedral_angle_3_deg	11.801
r_dihedral_angle_1_deg	5.944
r_scangle_it	2.688
r_scbond_it	1.636
r_angle_refined_deg	1.214
r_mcangle_it	0.945
r_mcbond_it	0.477
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.781
r_dihedral_angle_4_deg	12.715
r_dihedral_angle_3_deg	11.801
r_dihedral_angle_1_deg	5.944
r_scangle_it	2.688
r_scbond_it	1.636
r_angle_refined_deg	1.214
r_mcangle_it	0.945
r_mcbond_it	0.477
r_nbtor_refined	0.305
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.148
r_symmetry_hbond_refined	0.141
r_metal_ion_refined	0.12
r_xyhbond_nbd_refined	0.1
r_chiral_restr	0.083
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4246
Nucleic Acid Atoms
Solvent Atoms	782
Heterogen Atoms	76

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction

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.