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Human prolyl endopeptidase (PREP) - complex with JP-6-1-7
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 2.28 46.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.351 α = 90 b = 66.875 β = 99.339 c = 157.494 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 1.73 43.9 94.5 0.242 0.261 0.097 1 6.8 7.1 149376 17.8
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 1.97 67.6 1.139 1.232 0.463 1 1.6 7
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 43.9 149376 7395 65.493 0.184 0.1805 0.1808 0.2473 0.2473 25.522
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] 0.27 -0.13 -0.397 0.161
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.13 r_dihedral_angle_3_deg 15.674 r_dihedral_angle_6_deg 15.365 r_dihedral_angle_other_2_deg 11.03 r_dihedral_angle_1_deg 8.26 r_lrange_it 5.418 r_lrange_other 5.379 r_scangle_it 3.516 r_scangle_other 3.5 r_angle_refined_deg 2.617
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.13 r_dihedral_angle_3_deg 15.674 r_dihedral_angle_6_deg 15.365 r_dihedral_angle_other_2_deg 11.03 r_dihedral_angle_1_deg 8.26 r_lrange_it 5.418 r_lrange_other 5.379 r_scangle_it 3.516 r_scangle_other 3.5 r_angle_refined_deg 2.617 r_mcangle_it 2.58 r_mcangle_other 2.58 r_scbond_it 2.337 r_scbond_other 2.31 r_mcbond_it 1.685 r_mcbond_other 1.671 r_angle_other_deg 0.856 r_nbd_other 0.298 r_symmetry_nbd_refined 0.285 r_symmetry_xyhbond_nbd_refined 0.24 r_nbd_refined 0.226 r_symmetry_nbd_other 0.212 r_nbtor_refined 0.197 r_xyhbond_nbd_refined 0.193 r_chiral_restr 0.118 r_symmetry_xyhbond_nbd_other 0.102 r_symmetry_nbtor_other 0.099 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 17019 Nucleic Acid Atoms Solvent Atoms 1319 Heterogen Atoms 199
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling MOLREP phasing