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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 = 44.895 α = 90 b = 65.714 β = 94.51 c = 58.268 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 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 30 95.1 0.04 14.5 2 21797 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 2.07 95.1 0.23 3.6 1
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-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 30 21797 1176 95.1 0.163 0.1753 0.226 0.2366 RANDOM 25.94
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] -0.02 0.09 0.21 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.951 r_scangle_it 3.507 r_scbond_it 2.236 r_mcangle_it 1.693 r_angle_refined_deg 1.567 r_mcbond_it 0.94 r_angle_other_deg 0.9 r_symmetry_vdw_other 0.27 r_nbd_other 0.239 r_symmetry_hbond_refined 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.951 r_scangle_it 3.507 r_scbond_it 2.236 r_mcangle_it 1.693 r_angle_refined_deg 1.567 r_mcbond_it 0.94 r_angle_other_deg 0.9 r_symmetry_vdw_other 0.27 r_nbd_other 0.239 r_symmetry_hbond_refined 0.22 r_symmetry_vdw_refined 0.218 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.19 r_chiral_restr 0.101 r_nbtor_other 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 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 2208 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing