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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 = 45.071 α = 90 b = 65.863 β = 101.66 c = 54.473 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 2.2 30 96.3 0.08 7.6 4.3 16331 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 2.29 89.4 0.39 2.7 1.3
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 14833 796 97.9 0.202 0.198 0.2044 0.279 0.2789 RANDOM 37.8
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] -1.1 -0.48 -1.03 1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.187 r_scangle_it 3.946 r_scbond_it 2.4 r_mcangle_it 1.784 r_angle_refined_deg 1.593 r_mcbond_it 0.977 r_angle_other_deg 0.911 r_symmetry_hbond_refined 0.347 r_symmetry_vdw_other 0.269 r_symmetry_vdw_refined 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.187 r_scangle_it 3.946 r_scbond_it 2.4 r_mcangle_it 1.784 r_angle_refined_deg 1.593 r_mcbond_it 0.977 r_angle_other_deg 0.911 r_symmetry_hbond_refined 0.347 r_symmetry_vdw_other 0.269 r_symmetry_vdw_refined 0.23 r_nbd_other 0.229 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.194 r_chiral_restr 0.099 r_nbtor_other 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 2184 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing