4JQO

Crystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in complex with citrulline and inorganic phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4H31PDB ENTRY 4H31

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5289Protein: 10 mg/ml in 10 mM Tris-HCl pH 8.3, 60 mM L-citrulline, 100 mM NaH2PO4, 500 mM NaCl and 5 mM b-mercaptoethanol. Crystallization condition: 0.1M Bis-Tris pH 6.5, 27% w/v PEG 3350, 0.2M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4349.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.418α = 90
b = 82.597β = 90
c = 171.968γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBE-LENSES2012-06-21SINGLE WAVELENGT
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.085098.50.1140.11421.44.36935268312-328.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.082.1298.50.6780.67823.43388

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4H312.08236.046480568264345997.20.1630.1630.16160.1892RANDOM36.1376
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]
-2.340.571.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.393
r_dihedral_angle_4_deg15.19
r_dihedral_angle_3_deg14.398
r_dihedral_angle_1_deg5.732
r_angle_refined_deg1.758
r_angle_other_deg1.277
r_chiral_restr0.106
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_bond_other_d0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.393
r_dihedral_angle_4_deg15.19
r_dihedral_angle_3_deg14.398
r_dihedral_angle_1_deg5.732
r_angle_refined_deg1.758
r_angle_other_deg1.277
r_chiral_restr0.106
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_bond_other_d0.008
r_gen_planes_other0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7768
Nucleic Acid Atoms
Solvent Atoms430
Heterogen Atoms99

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
CCP4phasing
Cootmodel building