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Crystal structure of Ornithine carbamoyltransferase from Brucella melitensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other MODEL IN DIFFERENT SPACE GROUP OBTAINED FROM IODIDE PHASING
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 BrmeB.00183.a.B1.PS01877 at 20.3 mg/mL, RigakuReagents JCSG+ screen, h8: 25% PEG3350, 200 mM sodium chloride, 100 mM Bis-Tris-HCl, pH 5.5, cryoprotection: 15% ethylene glycol in two steps, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.28 46.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.45 α = 90 b = 88.45 β = 90 c = 142.68 γ = 120
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 ADSC QUANTUM 315r 2013-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0000 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.5 50 99.5 0.044 16.38 3.6 100819 100352 -3 23.829
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 99.2 0.39 2.43
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 MODEL IN DIFFERENT SPACE GROUP OBTAINED FROM IODIDE PHASING 1.5 50 100819 100315 4848 99.54 0.1559 0.1559 0.1546 0.1544 0.1826 0.1819 RANDOM 19.044
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] -0.4 -0.2 -0.4 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.101 r_dihedral_angle_4_deg 19.553 r_dihedral_angle_3_deg 12.072 r_dihedral_angle_1_deg 5.755 r_angle_refined_deg 1.556 r_mcangle_it 1.409 r_mcbond_it 0.869 r_angle_other_deg 0.859 r_mcbond_other 0.856 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.101 r_dihedral_angle_4_deg 19.553 r_dihedral_angle_3_deg 12.072 r_dihedral_angle_1_deg 5.755 r_angle_refined_deg 1.556 r_mcangle_it 1.409 r_mcbond_it 0.869 r_angle_other_deg 0.859 r_mcbond_other 0.856 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4556 Nucleic Acid Atoms Solvent Atoms 711 Heterogen Atoms 18
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction BOS data collection XDS data reduction