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Human prolyl endopeptidase (PREP) - complex with KT-2-108
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
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.189 α = 90 b = 67.075 β = 99.198 c = 157.164 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 1.83 43.9 92.1 0.237 0.256 0.097 0.99 6.6 6.8 144444 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 1.83 2 1.42 1.536 0.589 0.38 1.4
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 1.83 43.9 144443 7173 74.441 0.177 0.1734 0.1734 0.2395 0.2399 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] 0.133 -0.067 -0.039 -0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.297 r_dihedral_angle_3_deg 16.122 r_dihedral_angle_6_deg 15.198 r_dihedral_angle_1_deg 8.141 r_lrange_it 5.515 r_lrange_other 5.515 r_scangle_it 3.256 r_scangle_other 3.256 r_dihedral_angle_other_2_deg 3.116 r_angle_refined_deg 2.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.297 r_dihedral_angle_3_deg 16.122 r_dihedral_angle_6_deg 15.198 r_dihedral_angle_1_deg 8.141 r_lrange_it 5.515 r_lrange_other 5.515 r_scangle_it 3.256 r_scangle_other 3.256 r_dihedral_angle_other_2_deg 3.116 r_angle_refined_deg 2.57 r_mcangle_it 2.495 r_mcangle_other 2.495 r_scbond_it 2.181 r_scbond_other 2.181 r_mcbond_it 1.641 r_mcbond_other 1.597 r_angle_other_deg 0.841 r_nbd_other 0.313 r_symmetry_nbd_refined 0.277 r_nbd_refined 0.232 r_symmetry_nbd_other 0.214 r_symmetry_xyhbond_nbd_refined 0.213 r_xyhbond_nbd_refined 0.202 r_nbtor_refined 0.196 r_metal_ion_refined 0.172 r_symmetry_xyhbond_nbd_other 0.146 r_chiral_restr 0.115 r_symmetry_nbtor_other 0.101 r_xyhbond_nbd_other 0.046 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 1389 Heterogen Atoms 268
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling MOLREP phasing