2OD0 | pdb_00002od0

The crystal structure of gene product VP1028 from Vibrio parahaemolyticus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52982 M Ammonium sulfate, 0.1 M Citrate buffer, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9658.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.458α = 90
b = 42.876β = 90
c = 157.9γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2006-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97980APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9579.0699.440.108208.32072120605226.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.95297.160.4942.16.71549

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)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 DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.9579.062060520605109199.440.201870.199650.210.245210.25RANDOM26.353
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]
0.870.35-1.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.826
r_dihedral_angle_3_deg14.54
r_dihedral_angle_4_deg8.087
r_dihedral_angle_1_deg5.156
r_scangle_it3.664
r_scbond_it2.738
r_mcangle_it1.546
r_angle_refined_deg1.38
r_mcbond_it1.37
r_angle_other_deg0.88
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1640
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building