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Human prolyl endopeptidase (PREP) - complex with KT-2-74
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 277 25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.18 43.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.822 α = 90 b = 66.473 β = 102.067 c = 156.856 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 16M 2024-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979338 NSLS-II 17-ID-2
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 1.41 34.6 93.5 0.173 0.187 0.07 1 7.5 7 320614 11.5
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 1.41 1.53 48.6 2.022 2.172 0.792 0.27 1.4 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 1.41 34.6 320614 16132 80.072 0.157 0.1551 0.155 0.1922 0.1922 18.008
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] -0.031 0.045 0.025 -0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.394 r_dihedral_angle_2_deg 15.211 r_dihedral_angle_3_deg 12.947 r_dihedral_angle_1_deg 6.903 r_lrange_other 6.195 r_lrange_it 6.194 r_scangle_it 4.163 r_scangle_other 4.163 r_dihedral_angle_other_2_deg 3.886 r_scbond_it 2.813
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.394 r_dihedral_angle_2_deg 15.211 r_dihedral_angle_3_deg 12.947 r_dihedral_angle_1_deg 6.903 r_lrange_other 6.195 r_lrange_it 6.194 r_scangle_it 4.163 r_scangle_other 4.163 r_dihedral_angle_other_2_deg 3.886 r_scbond_it 2.813 r_scbond_other 2.813 r_angle_refined_deg 2.181 r_mcangle_it 1.86 r_mcangle_other 1.86 r_mcbond_it 1.279 r_mcbond_other 1.255 r_angle_other_deg 0.753 r_symmetry_xyhbond_nbd_refined 0.338 r_symmetry_nbd_refined 0.303 r_symmetry_xyhbond_nbd_other 0.27 r_nbd_refined 0.219 r_nbd_other 0.215 r_xyhbond_nbd_refined 0.198 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.185 r_chiral_restr 0.113 r_symmetry_nbtor_other 0.087 r_xyhbond_nbd_other 0.054 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 17030 Nucleic Acid Atoms Solvent Atoms 2323 Heterogen Atoms 304
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling MOLREP phasing