3UPD

2.9 Angstrom Crystal Structure of Ornithine Carbamoyltransferase (ArgF) from Vibrio vulnificus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DUV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7295Protein: 7.2mG/mL, 0.25M Sodium chloride, 0.01M Tris-HCl (pH 8.3); Screen: Calssics II (C2), 1.1M Ammonium tartrate (pH 7.0); Cryo: 4.0M Sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.8467.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.963α = 90
b = 153.963β = 90
c = 153.963γ = 90
Symmetry
Space GroupI 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMirrors2011-11-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.97903APS21-ID-D

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
12.9301000.09518.361353313533-382.7
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)
12.92.951000.5973.36642

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 REPLACEMENTTHROUGHOUT1DUV2.9128.11128611286166999.980.159780.159780.157990.19452RANDOM58.788
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.981
r_dihedral_angle_4_deg15.637
r_dihedral_angle_3_deg10.731
r_scangle_it4.376
r_scbond_it2.747
r_dihedral_angle_1_deg1.898
r_mcangle_it1.731
r_angle_refined_deg1.488
r_angle_other_deg0.885
r_mcbond_it0.882
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.981
r_dihedral_angle_4_deg15.637
r_dihedral_angle_3_deg10.731
r_scangle_it4.376
r_scbond_it2.747
r_dihedral_angle_1_deg1.898
r_mcangle_it1.731
r_angle_refined_deg1.488
r_angle_other_deg0.885
r_mcbond_it0.882
r_mcbond_other0.153
r_chiral_restr0.094
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2698
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling