4H31

Crystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in complex with carbamoyl phosphate and L-norvaline


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UPD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.5289Protein: 10 mg/ml in 10 mM Tris-HCl pH 8.3, 20 mM Carbamoyl phosphate, 20 mM L-norvaline, 500 mM NaCl and 5 mM b-mercaptoethanol. Crystallization condition: 0.2 M Ammonium Acetate, 0.1 M Bis-Tris pH 5.5, 23% PEG 3350, VAPOR DIFFUSION, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
1.9336.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.262α = 90
b = 80.911β = 90
c = 152.733γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBe-Lenses2012-06-21MSINGLE 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
11.7501000.0820.08229.86.5102701102659-321.9
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)
11.71.731000.9630.9631.95.55067

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 REPLACEMENTTHROUGHOUT3UPD1.7509675096702508899.950.137040.137040.135410.16735RANDOM25.753
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]
-1-0.041.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.631
r_dihedral_angle_4_deg14.34
r_dihedral_angle_3_deg13.539
r_dihedral_angle_1_deg5.718
r_angle_refined_deg1.799
r_angle_other_deg1.049
r_chiral_restr0.112
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.631
r_dihedral_angle_4_deg14.34
r_dihedral_angle_3_deg13.539
r_dihedral_angle_1_deg5.718
r_angle_refined_deg1.799
r_angle_other_deg1.049
r_chiral_restr0.112
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7712
Nucleic Acid Atoms
Solvent Atoms495
Heterogen Atoms206

Software

Software
Software NamePurpose
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
REFMACrefinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling