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Prolyl oligopeptidase B from Galerina marginata - apo protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 30% PEG4000 and 100 mM MES buffer, pH 6.5.
Crystal Properties Matthews coefficient Solvent content 2.55 51.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.89 α = 90 b = 105.62 β = 90 c = 86.96 γ = 90
Symmetry Space Group P 21 21 2
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 6M 2015-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
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 2.4 54 98.6 14.5 5.1 31438
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.4 54 29853 1584 94.07 0.2176 0.2156 0.25374 0.2326 RANDOM 44.333
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] 1.95 2.03 -3.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.59 r_dihedral_angle_3_deg 12.342 r_long_range_B_other 10.324 r_long_range_B_refined 10.323 r_dihedral_angle_4_deg 10.303 r_dihedral_angle_1_deg 6.328 r_mcangle_it 2.003 r_mcangle_other 2.003 r_scangle_other 1.701 r_angle_refined_deg 1.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.59 r_dihedral_angle_3_deg 12.342 r_long_range_B_other 10.324 r_long_range_B_refined 10.323 r_dihedral_angle_4_deg 10.303 r_dihedral_angle_1_deg 6.328 r_mcangle_it 2.003 r_mcangle_other 2.003 r_scangle_other 1.701 r_angle_refined_deg 1.171 r_mcbond_it 1.141 r_mcbond_other 1.141 r_scbond_it 0.998 r_scbond_other 0.998 r_angle_other_deg 0.87 r_chiral_restr 0.071 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 5578 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing