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Structure-Based Design of Novel PIN1 Inhibitors (I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IK8 PDB ENTRY 3IK8 Apo PPIase K7782Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 286 0.2M ammonium sulfate, 0.9M Na Citrate, 5mM TCEP, 100mM HEPES: Compound @ 500uM soaked into apo crystal for 60hrs. , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Crystal Properties Matthews coefficient Solvent content 1.77 38.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.255 α = 90 b = 36.53 β = 100.4 c = 51.32 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 110 IMAGE PLATE MAR scanner 345 mm plate OSMIC BLUE 2000-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R 1.0
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 1.86 10 99.1 0.061 20.7 4.39 18140 18140 1 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.93 91.5 0.404 0.404 3.6 4.2 1684
Refinement Statistics Diffraction ID Structure Solution 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION DIFFERENCE FOURIER PDB ENTRY 3IK8 Apo PPIase K7782Q 1.86 10 18140 18140 99.6 0.2062 0.2062 0.2062 0.1824 None selected
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 2001
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.076 s_non_zero_chiral_vol 0.035 s_zero_chiral_vol 0.029 s_from_restr_planes 0.0255 s_angle_d 0.02 s_anti_bump_dis_restr 0.019 s_bond_d 0.005 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1781 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 54
Software Software Software Name Purpose HKL-2000 data collection SHELX model building SHELXL-97 refinement DENZO data reduction SCALEPACK data scaling SHELX phasing