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Structure-guided design of alpha-amino acid-derived Pin1 inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PIN PDB ENTRY 1PIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 2.2M Ammonium sulphate, 0.1M HEPES buffer, 1% PEG 400, 5mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.91 57.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.354 α = 90 b = 68.354 β = 90 c = 79.849 γ = 120
Symmetry Space Group P 31 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 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2009-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 27.8 95.9 0.04 8.3 3.1 16739 16739 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.97 97.9 0.239 2.5 2.7 1436
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PIN 1.9 25 15882 15882 852 95.91 0.21672 0.21672 0.21475 0.2135 0.25376 0.2528 RANDOM 31.905
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] 1.46 0.73 1.46 -2.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.18 r_dihedral_angle_4_deg 18.205 r_dihedral_angle_3_deg 14.404 r_dihedral_angle_1_deg 6.395 r_scangle_it 3.88 r_scbond_it 2.614 r_mcangle_it 1.563 r_angle_refined_deg 1.466 r_mcbond_it 0.963 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.18 r_dihedral_angle_4_deg 18.205 r_dihedral_angle_3_deg 14.404 r_dihedral_angle_1_deg 6.395 r_scangle_it 3.88 r_scbond_it 2.614 r_mcangle_it 1.563 r_angle_refined_deg 1.466 r_mcbond_it 0.963 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.267 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.202 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1154 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 37
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement d*TREK data reduction d*TREK data scaling