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High Resolution Crystal Structure of Putative Pterin Binding Protein (PruR) from Vibrio cholerae O1 biovar El Tor str. N16961 in Complex with Neopterin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 Protein: 8.8 mg/ml, 0.01M Tris pH 8.3, 2mM Neopterin;
Screen: Classics II (D11), 0.1M Bis-Tris pH 6.5, 28% (w/v) PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 1.94 36.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.488 α = 90 b = 54.616 β = 91.5 c = 33.448 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 Be 2019-07-24 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) 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 1.03 30 96.5 0.092 0.092 0.105 0.049 22.1 4.6 57114 -3 7.9
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 1.03 1.05 93.4 0.764 0.764 0.867 0.404 0.719 3.2 4.3
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 1.03 21.48 54176 2929 96.3 0.1286 0.1276 0.1269 0.1467 0.1456 RANDOM 10.534
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] 0.13 -0.08 -0.52 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 8.219 r_dihedral_angle_1_deg 4.794 r_dihedral_angle_2_deg 3.718 r_rigid_bond_restr 2.135 r_angle_refined_deg 1.271 r_angle_other_deg 0.417 r_chiral_restr 0.065 r_gen_planes_refined 0.019 r_gen_planes_other 0.018 r_bond_refined_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 8.219 r_dihedral_angle_1_deg 4.794 r_dihedral_angle_2_deg 3.718 r_rigid_bond_restr 2.135 r_angle_refined_deg 1.271 r_angle_other_deg 0.417 r_chiral_restr 0.065 r_gen_planes_refined 0.019 r_gen_planes_other 0.018 r_bond_refined_d 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1096 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing