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Human prolyl endopeptidase (PREP) - complex with KT-2-59
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 2.27 45.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.888 α = 90 b = 67.026 β = 99.41 c = 157.386 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 2024-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979340 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 1.94 34.1 86.2 0.125 0.144 0.07 1 7.7 4.1 112416 26.7
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 1.94 2.12 42.4 0.967 1.08 0.474 0.54 1.7
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.94 34.1 106879 5537 70.04 0.15933 0.15549 0.1653 0.23309 0.2347 RANDOM 35.677
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] -0.13 -0.19 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.208 r_dihedral_angle_3_deg 17.001 r_dihedral_angle_1_deg 8.51 r_long_range_B_refined 6.946 r_long_range_B_other 6.946 r_scangle_other 4.914 r_scbond_it 3.402 r_scbond_other 3.401 r_mcangle_it 3.393 r_mcangle_other 3.393
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.208 r_dihedral_angle_3_deg 17.001 r_dihedral_angle_1_deg 8.51 r_long_range_B_refined 6.946 r_long_range_B_other 6.946 r_scangle_other 4.914 r_scbond_it 3.402 r_scbond_other 3.401 r_mcangle_it 3.393 r_mcangle_other 3.393 r_angle_refined_deg 2.674 r_mcbond_it 2.384 r_mcbond_other 2.378 r_angle_other_deg 0.875 r_chiral_restr 0.122 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17019 Nucleic Acid Atoms Solvent Atoms 1372 Heterogen Atoms 190
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction autoPROC data scaling MOLREP phasing