4JHX

Crystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in complex with carbamoylphosphate and arginine


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, 20 mM Carbamoyl phosphate, 60 mM Arginine, 500 mM NaCl and 5 mM b-mercaptoethanol. Crystallization condition: 0.1M Bis-Tris pH 6.5, 25% w/v PEG 3350, 0.2M Ammonium Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
1.8734.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.029α = 90
b = 79.387β = 90
c = 147.169γ = 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 WAVELENGTH
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
11.855099.90.0930.09331.96.57748877411-326.2
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)
11.851.8899.80.8630.8632.15.83799

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 4H311.8536.617676176638384899.840.15590.15590.15410.1897RANDOM32.7125
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]
-0.18-0.670.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.681
r_dihedral_angle_4_deg19.272
r_dihedral_angle_3_deg14.01
r_dihedral_angle_1_deg5.664
r_angle_refined_deg1.773
r_angle_other_deg1.42
r_chiral_restr0.114
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.681
r_dihedral_angle_4_deg19.272
r_dihedral_angle_3_deg14.01
r_dihedral_angle_1_deg5.664
r_angle_refined_deg1.773
r_angle_other_deg1.42
r_chiral_restr0.114
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.009
r_gen_planes_other0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7595
Nucleic Acid Atoms
Solvent Atoms571
Heterogen Atoms39

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