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Prolyl oligopeptidase B from Galerina marginata bound to 35mer hydrolysis and macrocyclization substrate - H698A mutant
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.7 293.15 27% PEGMME2000, 90 mM Bicine pH 8.7, 100 mM potassium thiocyanate, and 12.5mM Hexammine cobalt chloride.
Crystals were cryoprotected with 13% glycerol.
Crystal Properties Matthews coefficient Solvent content 2.25 45.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.18 α = 90 b = 115 β = 90 c = 141.45 γ = 90
Symmetry Space Group P 21 21 21
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 RIGAKU SATURN 944 2016-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.08 31.99 93.4 2.81 1.8 91770
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 MOLECULAR REPLACEMENT THROUGHOUT 2.9 89.23 32664 1690 93.93 0.25096 0.24868 0.2522 0.29547 0.3039 RANDOM 32.042
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] -2.18 -2.87 5.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.109 r_dihedral_angle_4_deg 12.376 r_dihedral_angle_3_deg 12.341 r_dihedral_angle_1_deg 5.89 r_long_range_B_refined 5.235 r_long_range_B_other 5.234 r_mcangle_other 2.64 r_mcangle_it 2.639 r_scangle_other 2.313 r_mcbond_it 1.541
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.109 r_dihedral_angle_4_deg 12.376 r_dihedral_angle_3_deg 12.341 r_dihedral_angle_1_deg 5.89 r_long_range_B_refined 5.235 r_long_range_B_other 5.234 r_mcangle_other 2.64 r_mcangle_it 2.639 r_scangle_other 2.313 r_mcbond_it 1.541 r_mcbond_other 1.534 r_scbond_it 1.349 r_scbond_other 1.348 r_angle_refined_deg 1.101 r_angle_other_deg 0.865 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11750 Nucleic Acid Atoms Solvent Atoms 939 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction Aimless data scaling PHASER phasing