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Crystal structure of dihydroorotase pyrC from Yersinia pestis in complex with zinc and malate at 2.4 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EG6 PDB entry 2EG6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 0.2 uL 10 mg/mL protein in 20 mM Tris-HCl pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP + 0.2 uL MCSG 2 condition #67 (0.15 M DL-malic acid, pH 7.0, 20% w/v PEG3350), equilibrated against 1.3 M sodium chloride solution in 96-well 3-drop crystallization plate (Swissci)
Crystal Properties Matthews coefficient Solvent content 2.26 45.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.838 α = 90 b = 112.202 β = 90 c = 208.264 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 PIXEL DECTRIS PILATUS3 X 6M 2016-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97923, 1.28241, 1.28908 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.4 50.01 93.8 0.088 0.088 0.096 0.037 7.5 6.1 81980 -3 41.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 94.1 0.622 0.622 0.68 0.265 0.778 2.1 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 2EG6 2.41 50.01 73934 3921 88.81 0.1613 0.1594 0.1648 0.1979 0.2051 RANDOM 44.305
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] 0.11 -0.14 0.04
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 46.284 r_dihedral_angle_2_deg 35.118 r_dihedral_angle_4_deg 15.444 r_dihedral_angle_3_deg 11.789 r_dihedral_angle_1_deg 5.432 r_angle_refined_deg 1.209 r_angle_other_deg 0.859 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 46.284 r_dihedral_angle_2_deg 35.118 r_dihedral_angle_4_deg 15.444 r_dihedral_angle_3_deg 11.789 r_dihedral_angle_1_deg 5.432 r_angle_refined_deg 1.209 r_angle_other_deg 0.859 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16072 Nucleic Acid Atoms Solvent Atoms 1064 Heterogen Atoms 57
Software Software Software Name Purpose LAUEGEN data processing SCALEPACK data scaling HKL-3000 data scaling MOLREP phasing HKL-3000 data reduction REFMAC refinement PDB_EXTRACT data extraction