Experiment: 1VK0

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	Sodium Citrate, Polyethylene glycol 2000, hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.831	α = 90
b = 120.831	β = 90
c = 185.222	γ = 120

Symmetry
Space Group	P 32 2 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	MARRESEARCH	Bent flat mirror and sagitally bent second crystal	2003-10-26	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-D	0.9792, 0.9800, 0.9641	APS	14-BM-D

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	2.1	35	100	0.062	29	10.6		91738

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	2.1	2.14	99.8		0.479	5.8	8.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.1	34.922	87085	4592	99.98	0.183	0.1829	0.1803	0.2326	RANDOM	30.501

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]
-0.008	-0.004		-0.008		0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	8.029
r_dihedral_angle_1_deg	6.716
r_scbond_it	5.826
r_mcangle_it	3.569
r_mcbond_it	1.982
r_angle_refined_deg	1.777
r_nbtor_refined	0.317
r_nbd_refined	0.21
r_symmetry_vdw_refined	0.205
r_symmetry_hbond_refined	0.171

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	8.029
r_dihedral_angle_1_deg	6.716
r_scbond_it	5.826
r_mcangle_it	3.569
r_mcbond_it	1.982
r_angle_refined_deg	1.777
r_nbtor_refined	0.317
r_nbd_refined	0.21
r_symmetry_vdw_refined	0.205
r_symmetry_hbond_refined	0.171
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.138
r_bond_refined_d	0.023
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9546
Nucleic Acid Atoms
Solvent Atoms	645
Heterogen Atoms

Software

Software
Software Name	Purpose
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction

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.