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Human Pin1 (Peptidyl-prolyl cis-trans isomerase) catalytic domain in complex with a covalent inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JYJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 (NH4)2SO4 0.2 M, Sodium citrate 1.2 M,HEPES 100 mM
Crystal Properties Matthews coefficient Solvent content 2.01 38.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.888 α = 90 b = 36.377 β = 100.984 c = 51.31 γ = 90
Symmetry Space Group C 1 2 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 CCD RIGAKU SATURN 944 2025-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.5
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 2 34.85 90.61 0.08085 0.08855 0.03553 0.996 18.59 6.1 13558 12.84
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.072 58.69 0.926
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 34.85 1.34 13388 683 90.37 0.2059 0.2053 0.2055 0.2173 0.2197 11.12
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.0586 f_angle_d 0.9206 f_chiral_restr 0.0461 f_plane_restr 0.0357 f_bond_d 0.0035
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1776 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement PHENIX refinement Aimless data scaling MOLREP phasing