3VB9 | pdb_00003vb9

Crystal structure of VPA0735 from Vibrio parahaemolyticus in monoclinic form, NorthEast Structural Genomics target VpR109

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2P3Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbatch under oil	7	277	200MM MOPS, PEG8000, MGCL2, 10MM DTT, PH 7.0, 0.5M lactose, Microbatch under oil, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.267	α = 90
b = 106.929	β = 94.8
c = 157.178	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	100	CCD	ADSC QUANTUM 4r		2011-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.979	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	2.09	50	95.9	0.076	11.4	2.5		237755			16.3

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	2.09	2.16	79.7		0.289	4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	2P3Y	2.1	39.99	2	118970	14075	89.9	0.224	0.224	0.22	0.274	0.28	RANDOM	25

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]
-2.98		4.042	11.842		-8.862

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.6
c_angle_deg	1.30103
c_improper_angle_d	0.9
c_bond_d	0.006204

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14887
Nucleic Acid Atoms
Solvent Atoms	839
Heterogen Atoms	7

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	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.