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Human prolyl endopeptidase (PREP) - complex with JP-2-1-7
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 2.17 43.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.337 α = 90 b = 66.845 β = 102.073 c = 155.637 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 1.85 42.7 94.1 0.26 0.28 0.15 0.99 6.1 7.1 131193 22.6
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 1.85 2.03 57.3 1.553 1.67 0.886 0.86 1.4 7.4
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 1.85 42.7 131193 6494 74.408 0.2 0.1964 0.196 0.2716 0.2716 30.465
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] -0.011 0.17 -0.559 0.455
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.892 r_dihedral_angle_3_deg 16.191 r_dihedral_angle_6_deg 15.346 r_dihedral_angle_1_deg 8.655 r_dihedral_angle_other_2_deg 6.021 r_lrange_it 5.901 r_lrange_other 5.901 r_scangle_it 3.718 r_scangle_other 3.699 r_mcangle_it 2.724
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.892 r_dihedral_angle_3_deg 16.191 r_dihedral_angle_6_deg 15.346 r_dihedral_angle_1_deg 8.655 r_dihedral_angle_other_2_deg 6.021 r_lrange_it 5.901 r_lrange_other 5.901 r_scangle_it 3.718 r_scangle_other 3.699 r_mcangle_it 2.724 r_mcangle_other 2.724 r_angle_refined_deg 2.673 r_scbond_it 2.459 r_scbond_other 2.451 r_mcbond_it 1.806 r_mcbond_other 1.756 r_angle_other_deg 0.869 r_nbd_other 0.255 r_nbd_refined 0.243 r_symmetry_xyhbond_nbd_other 0.236 r_symmetry_nbd_other 0.22 r_symmetry_xyhbond_nbd_refined 0.211 r_xyhbond_nbd_refined 0.203 r_nbtor_refined 0.201 r_symmetry_nbd_refined 0.2 r_chiral_restr 0.119 r_symmetry_nbtor_other 0.1 r_bond_refined_d 0.016 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 967 Heterogen Atoms 264
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling MOLREP phasing