☰ Navigation Tabs
Crystal structure of prolyl oligopeptidase from Microbulbifer arenaceous complex with a transition state analog inhibitor ZPR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VGB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.04M MES monohydrate pH 6.0, 8.8% (v/v) Polyethylene glycol 400
Crystal Properties Matthews coefficient Solvent content 2.26 45.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.108 α = 90 b = 65.622 β = 105.29 c = 91.765 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 0.979 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 2.722 30.96 96.28 0.924 5.75 5.1 18620
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 2.722 2.82 0.924
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7VGB 2.722 30.96 18608 931 96.352 0.199 0.1952 0.2708 0.2413 44.608
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] -0.225 -0.984 -0.297 0.922
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.723 r_dihedral_angle_3_deg 18.201 r_dihedral_angle_4_deg 15.886 r_dihedral_angle_1_deg 7.923 r_lrange_it 6.893 r_mcangle_it 4.311 r_scangle_it 4.251 r_scbond_it 2.81 r_mcbond_it 2.693 r_angle_refined_deg 1.242
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.723 r_dihedral_angle_3_deg 18.201 r_dihedral_angle_4_deg 15.886 r_dihedral_angle_1_deg 7.923 r_lrange_it 6.893 r_mcangle_it 4.311 r_scangle_it 4.251 r_scbond_it 2.81 r_mcbond_it 2.693 r_angle_refined_deg 1.242 r_nbtor_refined 0.324 r_symmetry_xyhbond_nbd_refined 0.248 r_nbd_refined 0.239 r_symmetry_nbd_refined 0.234 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.101 r_gen_planes_refined 0.005 r_bond_refined_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5439 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing