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Crystal structure of dihydroorotase pyrC from Vibrio cholerae in complex with zinc at 1.95 A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V0G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCE, and 20 mM L-citruline were mixed with 0.2 ul of the Top96 screen condition #C11 (0.2 M Sodium Acetate 0.1 M Sodium Cacodylate: HCl, pH 6.5 30 % (w/v) PEG 8000), 0.1 ul of the Hampton Additive screen # 94 (7%v/v 1-Butanol) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 1 hours.
Crystal Properties Matthews coefficient Solvent content 2 38.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.507 α = 90 b = 57.257 β = 105.09 c = 87.524 γ = 90
Symmetry Space Group P 1 21 1
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 Beryllium Lenses 2017-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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) CC (Half) 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 1.95 20 94.1 0.063 0.063 0.075 0.04 0.87 11.4 3.3 41257 -3 32.8
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 1.95 1.98 62.5 0.372 0.372 0.454 0.257 0.871 2.3 2.6
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 5V0G 1.95 20 39091 2077 93.97 0.1695 0.1676 0.1755 0.203 0.2103 RANDOM 48.505
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] 0.3 0.65 5.04 -4.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.157 r_sphericity_bonded 20.358 r_dihedral_angle_4_deg 15.236 r_dihedral_angle_3_deg 11.708 r_dihedral_angle_1_deg 6.003 r_angle_refined_deg 1.349 r_angle_other_deg 0.971 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_bond_other_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.157 r_sphericity_bonded 20.358 r_dihedral_angle_4_deg 15.236 r_dihedral_angle_3_deg 11.708 r_dihedral_angle_1_deg 6.003 r_angle_refined_deg 1.349 r_angle_other_deg 0.971 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_bond_other_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5118 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 21
Software Software Software Name Purpose MD2 data collection SCALEPACK data scaling HKL-3000 data reduction MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction