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Human prolyl endopeptidase (PREP) - complex with JP-7-1-7
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 2.16 43.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.543 α = 90 b = 66.302 β = 102.102 c = 156.244 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 EIGER X 9M 2025-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.919901 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 1.73 34.5 93.9 0.358 0.387 0.144 0.99 4.7 7.1 139379 15.1
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 1.73 1.99 55.7 1.472 1.587 0.588 0.5 1.5 7.2
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 1.73 34.5 139379 6975 64.265 0.192 0.1891 0.157 0.2554 0.214 18.159
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] -0.535 -0.165 -1.786 2.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.899 r_dihedral_angle_6_deg 14.697 r_dihedral_angle_2_deg 12.885 r_dihedral_angle_1_deg 7.91 r_lrange_it 3.109 r_lrange_other 3.034 r_scangle_it 2.005 r_scangle_other 2.005 r_angle_refined_deg 1.998 r_mcangle_it 1.522
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.899 r_dihedral_angle_6_deg 14.697 r_dihedral_angle_2_deg 12.885 r_dihedral_angle_1_deg 7.91 r_lrange_it 3.109 r_lrange_other 3.034 r_scangle_it 2.005 r_scangle_other 2.005 r_angle_refined_deg 1.998 r_mcangle_it 1.522 r_mcangle_other 1.522 r_scbond_it 1.321 r_scbond_other 1.321 r_mcbond_it 1.042 r_mcbond_other 1.035 r_angle_other_deg 0.663 r_symmetry_xyhbond_nbd_refined 0.271 r_xyhbond_nbd_refined 0.234 r_nbd_other 0.232 r_nbd_refined 0.21 r_symmetry_nbd_other 0.206 r_symmetry_nbd_refined 0.196 r_nbtor_refined 0.189 r_symmetry_xyhbond_nbd_other 0.095 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.089 r_xyhbond_nbd_other 0.016 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17019 Nucleic Acid Atoms Solvent Atoms 1638 Heterogen Atoms 413
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling MOLREP phasing