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DISCOVERY OF CELL-ACTIVE PHENYL-IMIDAZOLE PIN1 INHIBITORS BY STRUCTURE-GUIDED FRAGMENT EVOLUTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KCE PDB ENTRY 3KCE
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 277.0K
Crystal Properties Matthews coefficient Solvent content 2.87 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.668 α = 90 b = 68.668 β = 90 c = 79.477 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 277 IMAGE PLATE RIGAKU IMAGE PLATE MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 30 97.1 0.09 5.8 2.21 14643 2
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 2 2.08 97.5 0.46 1.5 2.15
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 3KCE 2 59.44 13886 736 96.91 0.22544 0.22258 0.2265 0.27699 0.2317 RANDOM 29.074
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] 0.76 0.38 0.76 -1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.636 r_dihedral_angle_4_deg 19.308 r_dihedral_angle_3_deg 18.22 r_dihedral_angle_1_deg 7.63 r_scangle_it 5.052 r_scbond_it 3.206 r_mcangle_it 2.037 r_angle_refined_deg 1.832 r_mcbond_it 1.145 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.636 r_dihedral_angle_4_deg 19.308 r_dihedral_angle_3_deg 18.22 r_dihedral_angle_1_deg 7.63 r_scangle_it 5.052 r_scbond_it 3.206 r_mcangle_it 2.037 r_angle_refined_deg 1.832 r_mcbond_it 1.145 r_chiral_restr 0.126 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1156 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling AMoRE phasing