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Crystal structure of prolyl oligopeptidase from Microbulbifer arenaceous complex with PEG400 and MES
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, HANGING DROP 6 277 0.04 M MES monohydrate pH 6.0, 8.8% (v/v) polyethylene glycol 400
Crystal Properties Matthews coefficient Solvent content 2.19 43.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.044 α = 90 b = 65.065 β = 104.948 c = 91.331 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 S 2M 2021-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17B1 0.97944 SSRF BL17B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.67 50 94.38 0.998 15.11 6.7 75931
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.7 0.899
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 THROUGHOUT 3MUN 1.67 31.651 75792 3688 94.38 0.161 0.1598 0.1598 0.1887 0.1887 16.037
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] 0.035 0.021 -0.128 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.162 r_dihedral_angle_4_deg 17.816 r_dihedral_angle_3_deg 13.35 r_dihedral_angle_1_deg 7.298 r_lrange_it 5.041 r_scangle_it 3.876 r_scbond_it 2.637 r_angle_refined_deg 2.222 r_mcangle_it 2.157 r_mcbond_it 1.447
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.162 r_dihedral_angle_4_deg 17.816 r_dihedral_angle_3_deg 13.35 r_dihedral_angle_1_deg 7.298 r_lrange_it 5.041 r_scangle_it 3.876 r_scbond_it 2.637 r_angle_refined_deg 2.222 r_mcangle_it 2.157 r_mcbond_it 1.447 r_nbtor_refined 0.351 r_nbd_refined 0.229 r_symmetry_nbd_refined 0.22 r_symmetry_xyhbond_nbd_refined 0.179 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.13 r_gen_planes_refined 0.013 r_bond_refined_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5414 Nucleic Acid Atoms Solvent Atoms 520 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing