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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 8.5 293 1.8M Ammonium citrate, 0.1M Tris buffer, 5mM DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 38.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.064 α = 90 b = 36.576 β = 101.11 c = 51.328 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 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2005-11-30 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 29.5 89.1 0.062 6.1 2.6 15369 15369 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 92 0.323 2.1 1.8 587
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PIN 2 29.49 13240 13240 726 94.12 0.17168 0.17168 0.16753 0.24876 0.2358 RANDOM 24.902
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] -0.04 -0.11 -0.05 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.358 r_dihedral_angle_4_deg 18.053 r_dihedral_angle_3_deg 15.858 r_dihedral_angle_1_deg 7.427 r_scangle_it 4.846 r_scbond_it 3.173 r_mcangle_it 1.834 r_angle_refined_deg 1.805 r_mcbond_it 1.073 r_chiral_restr 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.358 r_dihedral_angle_4_deg 18.053 r_dihedral_angle_3_deg 15.858 r_dihedral_angle_1_deg 7.427 r_scangle_it 4.846 r_scbond_it 3.173 r_mcangle_it 1.834 r_angle_refined_deg 1.805 r_mcbond_it 1.073 r_chiral_restr 0.129 r_bond_refined_d 0.021 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1795 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 28
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement d*TREK data reduction d*TREK data scaling