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Human prolyl endopeptidase (PREP) - complex with KYP2047
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 in 25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.16 43.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.582 α = 90 b = 66.227 β = 102.194 c = 156.431 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 2024-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97934 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 1.58 34.5 89.9 0.125 0.151 0.083 0.99 5.4 3.1 189386 14.1
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 1.58 1.78 0.754 0.925 0.527 0.45 1.5
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 1.58 34.5 189385 9492 66.286 0.152 0.1499 0.1504 0.2001 0.2007 20.421
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] 0.282 -0.433 0.361 -0.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.301 r_dihedral_angle_3_deg 13.758 r_dihedral_angle_2_deg 11.835 r_dihedral_angle_1_deg 7.256 r_lrange_it 6.093 r_lrange_other 6.092 r_scangle_it 4.338 r_scangle_other 4.337 r_scbond_it 2.848 r_scbond_other 2.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.301 r_dihedral_angle_3_deg 13.758 r_dihedral_angle_2_deg 11.835 r_dihedral_angle_1_deg 7.256 r_lrange_it 6.093 r_lrange_other 6.092 r_scangle_it 4.338 r_scangle_other 4.337 r_scbond_it 2.848 r_scbond_other 2.848 r_angle_refined_deg 2.361 r_mcangle_it 2.092 r_mcangle_other 2.092 r_mcbond_it 1.45 r_mcbond_other 1.431 r_angle_other_deg 0.801 r_symmetry_xyhbond_nbd_refined 0.256 r_nbd_other 0.23 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.209 r_symmetry_nbd_refined 0.205 r_chiral_restr 0.202 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.19 r_symmetry_nbtor_other 0.093 r_symmetry_xyhbond_nbd_other 0.05 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17031 Nucleic Acid Atoms Solvent Atoms 2051 Heterogen Atoms 221
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing