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Human prolyl endopeptidase (PREP) - complex with KT-2-197
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 43.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.445 α = 90 b = 66.247 β = 102.004 c = 156.2 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 1.66 34.5 95.2 0.248 0.267 0.1 0.99 6.5 7 184521 13.9
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 1.66 1.84 55.6 1.425 1.544 0.589 0.34 1.4 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 1.66 34.5 184521 9156 75.401 0.164 0.1616 0.1618 0.2159 0.2158 18.612
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] 0.008 -0.132 0.069 -0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.545 r_dihedral_angle_3_deg 14.448 r_dihedral_angle_2_deg 13.231 r_dihedral_angle_1_deg 7.362 r_lrange_it 5.469 r_lrange_other 5.398 r_scangle_it 3.805 r_scangle_other 3.805 r_scbond_it 2.591 r_scbond_other 2.591
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.545 r_dihedral_angle_3_deg 14.448 r_dihedral_angle_2_deg 13.231 r_dihedral_angle_1_deg 7.362 r_lrange_it 5.469 r_lrange_other 5.398 r_scangle_it 3.805 r_scangle_other 3.805 r_scbond_it 2.591 r_scbond_other 2.591 r_angle_refined_deg 2.323 r_mcangle_it 1.893 r_mcangle_other 1.893 r_mcbond_it 1.313 r_mcbond_other 1.309 r_angle_other_deg 0.776 r_nbd_other 0.261 r_nbd_refined 0.218 r_symmetry_xyhbond_nbd_refined 0.213 r_symmetry_nbd_other 0.204 r_xyhbond_nbd_refined 0.193 r_nbtor_refined 0.191 r_symmetry_nbd_refined 0.163 r_symmetry_xyhbond_nbd_other 0.137 r_chiral_restr 0.113 r_symmetry_nbtor_other 0.094 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 1661 Heterogen Atoms 419
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling MOLREP phasing