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Structure-based design of C8-substituted O6-cyclohexylmethoxyguanine CDK1 and 2 inhibitors.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H1S PDB ENTRY 1H1S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 50 MM AMMONIUM ACETATE, 10% PEG-3350, 15 MM NACL, 100 MM HEPES, PH = 7.4, 10% DMSO
Crystal Properties Matthews coefficient Solvent content 2.82 56.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.806 α = 90 b = 133.744 β = 90 c = 147.46 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX SX-165mm M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R ELETTRA 5.2R
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 19.8 99.6 0.07 11.9 3.24 74525
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 2.32 100 0.36 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 1H1S 2.2 19.82 70608 3750 99.37 0.18383 0.18185 0.1888 0.22071 0.224 RANDOM 35.756
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] -0.91 0.81 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.456 r_dihedral_angle_4_deg 20.703 r_dihedral_angle_3_deg 16.9 r_dihedral_angle_1_deg 6.282 r_angle_other_deg 2.464 r_angle_refined_deg 1.926 r_mcangle_it 1.435 r_scbond_it 1.232 r_mcbond_it 0.962 r_mcbond_other 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.456 r_dihedral_angle_4_deg 20.703 r_dihedral_angle_3_deg 16.9 r_dihedral_angle_1_deg 6.282 r_angle_other_deg 2.464 r_angle_refined_deg 1.926 r_mcangle_it 1.435 r_scbond_it 1.232 r_mcbond_it 0.962 r_mcbond_other 0.96 r_chiral_restr 0.125 r_bond_refined_d 0.018 r_gen_planes_other 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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_mcangle_other r_scbond_other r_scangle_it 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 8819 Nucleic Acid Atoms Solvent Atoms 489 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement PHASER phasing