3NLC | pdb_00003nlc

Crystal structure of the VP0956 protein from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium Target VpR147

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microbatch under Paraffin oil	9	291	20% PEG 4000, 0.1M magnesium sulfate, 0.001M FAD, 0.1M TAPS, pH 9.0, microbatch under Paraffin oil, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.079	α = 90
b = 78.166	β = 90
c = 101.875	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 4		2010-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.97907	NSLS	X4A

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	2.15	50	98.4	0.067	34.1	6.8	57928	57001

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)
	2.15	2.23	99.8		0.492	4.9	6.5	5796

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	SAD	THROUGHOUT	2.15	36.49	0.92	56907	2868	98.19	0.2182	0.2153	0.2129	0.2709	0.2669	RANDOM

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]
-9.4844			13.4429		-3.9585

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.916
f_angle_d	1.21
f_chiral_restr	0.08
f_bond_d	0.009
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4060
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	53

Software

Software
Software Name	Purpose
ADSC	data collection
SHELXDE	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

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.