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High Resolution Crystal Structure of Putative Pterin Binding Protein PruR (VV2_1280) from Vibrio vulnificus CMCP6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 292 Protein: 7.2 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3);
Screen: Classics II (A7), 0.1M Citric acid (pH 3.5), 3.0M Sodium chloride.
Cryo: 4.0M Formate
Crystal Properties Matthews coefficient Solvent content 2 38.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.046 α = 90 b = 71.087 β = 90 c = 106.359 γ = 90
Symmetry Space Group I 2 2 2
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 2018-11-15 M SINGLE WAVELENGTH
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) 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 0.99 30 93.4 0.075 0.075 0.081 0.03 45.1 7.3 65367 -3 6.8
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 0.99 1.01 82.2 0.679 0.679 0.74 0.288 0.821 3.2 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 0.99 26.6 62187 3176 93.21 0.1205 0.1195 0.119 0.141 0.1403 RANDOM 9.117
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] -1.07 0.61 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.417 r_dihedral_angle_4_deg 13.304 r_dihedral_angle_3_deg 9.826 r_rigid_bond_restr 9.196 r_dihedral_angle_1_deg 4.926 r_angle_refined_deg 1.53 r_angle_other_deg 1.389 r_chiral_restr 0.084 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.417 r_dihedral_angle_4_deg 13.304 r_dihedral_angle_3_deg 9.826 r_rigid_bond_restr 9.196 r_dihedral_angle_1_deg 4.926 r_angle_refined_deg 1.53 r_angle_other_deg 1.389 r_chiral_restr 0.084 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1098 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing