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Bacterial prolidase mutant D45W/L225Y/H226L/H343I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AH8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100mM MES (pH6.5), 5% (v/v) PEG 400, 2M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.9 57.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.965 α = 90 b = 182.965 β = 90 c = 372.079 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 PIXEL DECTRIS EIGER X 16M 2018-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97918 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.22 67.45 93.9 0.13 0.134 0.03 0.998 15.9 20.1 111133
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.22 2.34 80.7 1.13 1.161 0.262 0.902 18.9
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 6AH8 2.22 67.45 105561 5564 93.88 0.2046 0.203 0.2108 0.2347 0.2402 RANDOM 47.012
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] 1.2 0.6 1.2 -3.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.33 r_dihedral_angle_4_deg 15.339 r_dihedral_angle_3_deg 14.234 r_dihedral_angle_1_deg 6.85 r_angle_other_deg 1.456 r_angle_refined_deg 1.447 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.33 r_dihedral_angle_4_deg 15.339 r_dihedral_angle_3_deg 14.234 r_dihedral_angle_1_deg 6.85 r_angle_other_deg 1.456 r_angle_refined_deg 1.447 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14271 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing