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Crystal structure of apo prolyl oligopeptidase from Microbulbifer arenaceous
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MUN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M Trimethylamine N-oxide dihydrate, 0.1M Tris pH 8.5, 20% (w/v) Polyethylene glycol monomethyl ether 2000
Crystal Properties Matthews coefficient Solvent content 2.19 43.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.39 α = 90 b = 125.395 β = 96.837 c = 89.848 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 PIXEL DECTRIS PILATUS3 6M 2020-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979 SSRF BL18U1
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 2.227 44.198 99.86 0.1398 0.1516 0.0581 0.994 12.53 6.8 64538 19.9
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 2.227 2.31 99.97 0.5265 0.5753 0.2292 0.899 4.37 6.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3MUN 2.227 44.198 64531 3237 99.744 0.155 0.1524 0.1532 0.2072 0.2077 21.548
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] 1.048 -1.486 -0.767 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.3 r_dihedral_angle_4_deg 17.429 r_dihedral_angle_3_deg 14.65 r_dihedral_angle_1_deg 7.209 r_lrange_it 5.373 r_scangle_it 3.582 r_mcangle_it 2.451 r_scbond_it 2.315 r_mcbond_it 1.547 r_angle_refined_deg 1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.3 r_dihedral_angle_4_deg 17.429 r_dihedral_angle_3_deg 14.65 r_dihedral_angle_1_deg 7.209 r_lrange_it 5.373 r_scangle_it 3.582 r_mcangle_it 2.451 r_scbond_it 2.315 r_mcbond_it 1.547 r_angle_refined_deg 1.43 r_nbtor_refined 0.313 r_symmetry_nbd_refined 0.203 r_nbd_refined 0.202 r_symmetry_xyhbond_nbd_refined 0.171 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.111 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10892 Nucleic Acid Atoms Solvent Atoms 1016 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing