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Crystal structure of PIN1 in complex with inhibitor C3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KAI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 0.1 M MES (pH 6.5), 0.2 M Ammonium sulfate, 24~33% (v/v) PEG5K MME
Crystal Properties Matthews coefficient Solvent content 2.83 56.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.59 α = 90 b = 176.64 β = 90 c = 42.63 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277 PIXEL DECTRIS PILATUS 6M 2022-12-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979183 SSRF BL18U1
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 1.93 34.554 100 0.188 0.992 8.1 12.4 32019
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 1.93 1.98 0.671
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 1.93 34.554 31962 1578 99.969 0.195 0.1929 0.1935 0.2295 0.2305 39.597
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] 1.811 -1.498 -0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.591 r_dihedral_angle_4_deg 16.03 r_dihedral_angle_3_deg 14.359 r_dihedral_angle_1_deg 7.296 r_lrange_it 7.242 r_lrange_other 7.192 r_scangle_it 6.068 r_scangle_other 6.037 r_scbond_it 4.266 r_scbond_other 4.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.591 r_dihedral_angle_4_deg 16.03 r_dihedral_angle_3_deg 14.359 r_dihedral_angle_1_deg 7.296 r_lrange_it 7.242 r_lrange_other 7.192 r_scangle_it 6.068 r_scangle_other 6.037 r_scbond_it 4.266 r_scbond_other 4.247 r_mcangle_it 4.073 r_mcangle_other 4.072 r_mcbond_it 3.136 r_mcbond_other 3.132 r_angle_refined_deg 1.78 r_angle_other_deg 1.394 r_nbd_other 0.224 r_symmetry_nbd_refined 0.21 r_symmetry_xyhbond_nbd_refined 0.21 r_nbd_refined 0.204 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.146 r_symmetry_xyhbond_nbd_other 0.126 r_chiral_restr 0.122 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_xyhbond_nbd_other 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2288 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALA data scaling MOLREP phasing