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Structure-based Design of Novel Chk1 Inhibitors: Insights into Hydrogen Bonding and Protein-Ligand Affinity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IA8 PDB ENTRY 1IA8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.9 56.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.116 α = 90 b = 65.909 β = 101.38 c = 54.582 γ = 90
Symmetry Space Group P 1 21 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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 2.12 30 96.1 0.05 10.2 5.1 17903 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 2.12 2.2 89.7 0.31 3.4 4.5
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 1IA8 2.2 30 14865 788 97.6 0.228 0.226 0.2272 0.281 0.282 RANDOM 35.48
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] -2.03 -1 -0.13 1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.381 r_angle_other_deg 1.089 r_scangle_it 1.086 r_angle_refined_deg 0.996 r_mcangle_it 0.833 r_scbond_it 0.602 r_mcbond_it 0.453 r_nbd_other 0.18 r_symmetry_vdw_other 0.163 r_nbd_refined 0.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.381 r_angle_other_deg 1.089 r_scangle_it 1.086 r_angle_refined_deg 0.996 r_mcangle_it 0.833 r_scbond_it 0.602 r_mcbond_it 0.453 r_nbd_other 0.18 r_symmetry_vdw_other 0.163 r_nbd_refined 0.158 r_symmetry_hbond_refined 0.146 r_symmetry_vdw_refined 0.119 r_xyhbond_nbd_refined 0.117 r_nbtor_other 0.079 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 2127 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing