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Human prolyl endopeptidase (PREP) - complex with YX45
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 45.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.22 α = 90 b = 66.877 β = 99.287 c = 156.909 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 2024-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9201 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 1.49 34.94 95 0.071 0.084 0.044 1 9.9 3.5 260713 17.4
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 1.49 1.53 68.1 0.768 0.913 0.488 0.54 1.5 3.4
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 1.49 34.94 260713 13016 73.439 0.165 0.1634 0.1635 0.2065 0.2066 23.52
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] 0.21 -0.199 -0.054 -0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.401 r_dihedral_angle_3_deg 13.818 r_dihedral_angle_2_deg 13.554 r_dihedral_angle_1_deg 7.082 r_lrange_it 5.951 r_lrange_other 5.951 r_scangle_it 4.209 r_scangle_other 4.209 r_scbond_it 2.83 r_scbond_other 2.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.401 r_dihedral_angle_3_deg 13.818 r_dihedral_angle_2_deg 13.554 r_dihedral_angle_1_deg 7.082 r_lrange_it 5.951 r_lrange_other 5.951 r_scangle_it 4.209 r_scangle_other 4.209 r_scbond_it 2.83 r_scbond_other 2.83 r_angle_refined_deg 2.316 r_mcangle_it 2.183 r_mcangle_other 2.183 r_mcbond_it 1.539 r_mcbond_other 1.539 r_angle_other_deg 0.783 r_symmetry_xyhbond_nbd_refined 0.275 r_symmetry_nbd_refined 0.271 r_nbd_other 0.269 r_nbd_refined 0.213 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.184 r_symmetry_xyhbond_nbd_other 0.169 r_chiral_restr 0.112 r_symmetry_nbtor_other 0.091 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 17017 Nucleic Acid Atoms Solvent Atoms 1975 Heterogen Atoms 245
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling MOLREP phasing