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Human prolyl endopeptidase (PREP) - complex with JP-4-1-7
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 2.29 46.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.853 α = 90 b = 67.294 β = 99.109 c = 158.019 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 2025-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.919764 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 2.01 44 93.4 0.273 0.294 0.11 0.99 5.9 7.1 106903 24.4
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 2.01 2.22 54.6 1.53 1.643 0.596 0.33 7.5
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 2.01 44 106903 5347 73.378 0.189 0.1845 0.1849 0.266 0.2664 34.517
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] 0.227 -0.617 -0.232 0.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.263 r_dihedral_angle_3_deg 17.767 r_dihedral_angle_6_deg 14.985 r_dihedral_angle_1_deg 9.409 r_dihedral_angle_other_2_deg 7.441 r_lrange_it 5.399 r_lrange_other 5.388 r_scangle_it 3.623 r_scangle_other 3.613 r_mcangle_it 3.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.263 r_dihedral_angle_3_deg 17.767 r_dihedral_angle_6_deg 14.985 r_dihedral_angle_1_deg 9.409 r_dihedral_angle_other_2_deg 7.441 r_lrange_it 5.399 r_lrange_other 5.388 r_scangle_it 3.623 r_scangle_other 3.613 r_mcangle_it 3.056 r_mcangle_other 3.056 r_angle_refined_deg 2.833 r_scbond_it 2.354 r_scbond_other 2.352 r_mcbond_it 1.985 r_mcbond_other 1.966 r_angle_other_deg 0.92 r_symmetry_xyhbond_nbd_refined 0.266 r_symmetry_nbd_refined 0.263 r_nbd_other 0.259 r_nbd_refined 0.236 r_symmetry_nbd_other 0.225 r_nbtor_refined 0.207 r_xyhbond_nbd_refined 0.196 r_chiral_restr 0.12 r_symmetry_nbtor_other 0.107 r_symmetry_xyhbond_nbd_other 0.101 r_xyhbond_nbd_other 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 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 739 Heterogen Atoms 157
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling MOLREP phasing