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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 56.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.986 α = 90 b = 65.733 β = 94.46 c = 58.494 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.1 30 96.7 0.06 13.6 4.1 19953 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 2.1 2.18 90.1 0.31 3.5 3.6
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 2.1 58.72 17743 1631 97.1 0.183 0.176 0.1855 0.257 0.2648 RANDOM 30.95
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] -0.6 0.12 0.33 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.641 r_scangle_it 4.335 r_scbond_it 2.857 r_angle_refined_deg 2.073 r_mcangle_it 1.999 r_angle_other_deg 1.289 r_mcbond_it 1.138 r_symmetry_hbond_refined 0.433 r_symmetry_vdw_other 0.296 r_nbd_other 0.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.641 r_scangle_it 4.335 r_scbond_it 2.857 r_angle_refined_deg 2.073 r_mcangle_it 1.999 r_angle_other_deg 1.289 r_mcbond_it 1.138 r_symmetry_hbond_refined 0.433 r_symmetry_vdw_other 0.296 r_nbd_other 0.248 r_symmetry_vdw_refined 0.234 r_xyhbond_nbd_refined 0.221 r_nbd_refined 0.217 r_chiral_restr 0.132 r_nbtor_other 0.092 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 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 2090 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing