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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 2.86 56.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.937 α = 90 b = 67.937 β = 90 c = 79.247 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 2006-11-03 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 2.3 27.6 96.2 0.081 4.6 2.9 9395 9395 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) 2.3 2.38 99.8 0.438 1.3 2.8 885
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 MIR THROUGHOUT PDB ENTRY 1PIN 2.3 27.6 8939 452 96.05 0.23048 0.22664 0.2203 0.31195 0.3065 RANDOM 46.677
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] 2.26 1.13 2.26 -3.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.744 r_dihedral_angle_4_deg 24.382 r_dihedral_angle_3_deg 17.609 r_dihedral_angle_1_deg 7.527 r_scangle_it 4.157 r_scbond_it 2.6 r_mcangle_it 1.983 r_angle_refined_deg 1.908 r_mcbond_it 1.094 r_chiral_restr 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.744 r_dihedral_angle_4_deg 24.382 r_dihedral_angle_3_deg 17.609 r_dihedral_angle_1_deg 7.527 r_scangle_it 4.157 r_scbond_it 2.6 r_mcangle_it 1.983 r_angle_refined_deg 1.908 r_mcbond_it 1.094 r_chiral_restr 0.117 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1152 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 26
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement d*TREK data reduction d*TREK data scaling