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Crystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in complex with citrulline and inorganic phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H31 PDB ENTRY 4H31
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 Protein: 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 coefficient Solvent content 2.43 49.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.418 α = 90 b = 82.597 β = 90 c = 171.968 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD BE-LENSES 2012-06-21 SINGLE WAVELENGT
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.08 50 98.5 0.114 0.114 21.4 4.3 69352 68312 -3 28.7
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) Redundancy Number Unique Reflections (All) 1 2.08 2.12 98.5 0.678 0.678 2 3.4 3388
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4H31 2.082 36.04 64805 68264 3459 97.2 0.163 0.163 0.1616 0.1709 0.1892 0.1994 RANDOM 36.1376
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] -2.34 0.57 1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.393 r_dihedral_angle_4_deg 15.19 r_dihedral_angle_3_deg 14.398 r_dihedral_angle_1_deg 5.732 r_angle_refined_deg 1.758 r_angle_other_deg 1.277 r_chiral_restr 0.106 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.393 r_dihedral_angle_4_deg 15.19 r_dihedral_angle_3_deg 14.398 r_dihedral_angle_1_deg 5.732 r_angle_refined_deg 1.758 r_angle_other_deg 1.277 r_chiral_restr 0.106 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.008 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7768 Nucleic Acid Atoms Solvent Atoms 430 Heterogen Atoms 99
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing MOLREP phasing CCP4 phasing Coot model building