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Prolyl oligopeptidase B from Galerina marginata bound to 35mer hydrolysis and macrocyclization substrate - S577A mutant
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.7 293.15 28% PEG6000, 100 mM Bicine pH 8.7, 64 mM Sodium Potassium Phosphate, 12.5mM Hexammine cobalt chloride, crystals cryoprotected with 12% glycerol
Crystal Properties Matthews coefficient Solvent content 2.44 49.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.797 α = 90 b = 142.562 β = 90.29 c = 116.356 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 PILATUS 6M-F 2016-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.920 Diamond I04-1
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 2.19 90.14 96.77 6.7 2 163136
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 2.19 90.14 155177 7959 96.77 0.21562 0.21391 0.2175 0.24944 0.25 RANDOM 32.215
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] 2.03 0.11 -3.17 1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.053 r_dihedral_angle_4_deg 14.672 r_dihedral_angle_3_deg 13.302 r_dihedral_angle_1_deg 6.124 r_long_range_B_refined 4.772 r_long_range_B_other 4.772 r_scangle_other 2.293 r_mcangle_it 1.879 r_mcangle_other 1.879 r_angle_refined_deg 1.423
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.053 r_dihedral_angle_4_deg 14.672 r_dihedral_angle_3_deg 13.302 r_dihedral_angle_1_deg 6.124 r_long_range_B_refined 4.772 r_long_range_B_other 4.772 r_scangle_other 2.293 r_mcangle_it 1.879 r_mcangle_other 1.879 r_angle_refined_deg 1.423 r_scbond_it 1.414 r_scbond_other 1.414 r_mcbond_it 1.118 r_mcbond_other 1.118 r_angle_other_deg 0.961 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 23876 Nucleic Acid Atoms Solvent Atoms 1196 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing