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Human prolyl endopeptidase (PREP) - complex with S17092
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DDU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.26 45.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.187 α = 81.782 b = 105.735 β = 89.794 c = 155.67 γ = 89.701
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 EIGER X 9M 2024-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9201 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.81 29.68 83.3 0.07 0.1 0.07 0.99 5.2 1.8 286151 22.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.81 1.93 53.3 0.371 0.524 0.371 0.62 1.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.81 29.68 286150 14477 74.078 0.194 0.1907 0.1898 0.2489 0.2479 25.592
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] 0.329 0.078 0.185 -0.566 0.008 0.231
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.82 r_dihedral_angle_6_deg 15.504 r_dihedral_angle_2_deg 13.757 r_dihedral_angle_1_deg 8.065 r_lrange_it 4.884 r_lrange_other 4.864 r_scangle_it 3.676 r_scangle_other 3.676 r_angle_refined_deg 2.617 r_scbond_it 2.518
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.82 r_dihedral_angle_6_deg 15.504 r_dihedral_angle_2_deg 13.757 r_dihedral_angle_1_deg 8.065 r_lrange_it 4.884 r_lrange_other 4.864 r_scangle_it 3.676 r_scangle_other 3.676 r_angle_refined_deg 2.617 r_scbond_it 2.518 r_scbond_other 2.517 r_mcangle_it 2.49 r_mcangle_other 2.49 r_mcbond_it 1.794 r_mcbond_other 1.787 r_angle_other_deg 0.866 r_symmetry_xyhbond_nbd_refined 0.266 r_nbd_other 0.258 r_symmetry_nbd_refined 0.244 r_nbd_refined 0.22 r_symmetry_nbd_other 0.211 r_nbtor_refined 0.197 r_xyhbond_nbd_refined 0.194 r_chiral_restr 0.124 r_symmetry_xyhbond_nbd_other 0.111 r_symmetry_nbtor_other 0.097 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 34038 Nucleic Acid Atoms Solvent Atoms 1747 Heterogen Atoms 281
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling MOLREP phasing