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Crystal structure of human PIN1 bound to compound 155
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VAJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 100 mM HEPES pH 7.5 200 mM ammonium sulphate 1.1-1.3 M sodium citrate 5 mM DTT
Crystal Properties Matthews coefficient Solvent content 1.82 32.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.114 α = 90 b = 36.274 β = 100.356 c = 51.957 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 PIXEL DECTRIS EIGER2 X 9M 2025-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87313 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 58.1 99.9 0.093 0.98 13.4 4.6 28927
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 1.6 1.7 99.9 0.98
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 1.6 58.095 28914 1400 99.938 0.191 0.1893 0.1897 0.2293 0.2297 21.174
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] 0.577 -0.2 0.032 -0.503
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.264 r_dihedral_angle_3_deg 12.933 r_dihedral_angle_2_deg 11.246 r_lrange_it 7.135 r_dihedral_angle_1_deg 6.672 r_scangle_it 6.057 r_scbond_it 4.197 r_mcangle_it 2.873 r_angle_refined_deg 2.211 r_mcbond_it 2.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.264 r_dihedral_angle_3_deg 12.933 r_dihedral_angle_2_deg 11.246 r_lrange_it 7.135 r_dihedral_angle_1_deg 6.672 r_scangle_it 6.057 r_scbond_it 4.197 r_mcangle_it 2.873 r_angle_refined_deg 2.211 r_mcbond_it 2.097 r_nbtor_refined 0.309 r_nbd_refined 0.21 r_symmetry_xyhbond_nbd_refined 0.195 r_symmetry_nbd_refined 0.193 r_chiral_restr 0.14 r_xyhbond_nbd_refined 0.136 r_bond_refined_d 0.013 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1785 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing