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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 57.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.504 α = 90 b = 68.504 β = 90 c = 79.56 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 2006-10-30 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 26 94.9 0.057 6.2 2 16604 16604 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 84.9 0.397 1.5 1.9 873
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PIN 1.9 26 15750 842 94.8 0.20511 0.20247 0.1999 0.25511 0.2536 RANDOM 31.787
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] 0.69 0.34 0.69 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.593 r_dihedral_angle_4_deg 19.189 r_dihedral_angle_3_deg 16.113 r_dihedral_angle_1_deg 7.385 r_scangle_it 6.043 r_scbond_it 3.682 r_mcangle_it 2.353 r_angle_refined_deg 1.974 r_mcbond_it 1.362 r_chiral_restr 0.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.593 r_dihedral_angle_4_deg 19.189 r_dihedral_angle_3_deg 16.113 r_dihedral_angle_1_deg 7.385 r_scangle_it 6.043 r_scbond_it 3.682 r_mcangle_it 2.353 r_angle_refined_deg 1.974 r_mcbond_it 1.362 r_chiral_restr 0.155 r_bond_refined_d 0.025 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1170 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 45
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement d*TREK data reduction d*TREK data scaling