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CDK2 in complex with the imidazole pyrimidine amide, compound (S)-8b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other INTERNAL CDK2 STRUCTURE MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 8% PEG 3350, 0.1M HEPES PH 7.5, 0.05M AMMONIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 2.06 40.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.542 α = 90 b = 71.824 β = 90 c = 71.771 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 RIGAKU SATURN 92 CONFOCAL MIRRORS (VARIMAX) 2005-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 2.15 50.77 99.7 0.1 6 3.33 15575 3 31
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 2.15 2.23 99.9 0.39 2.1 3.3
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT INTERNAL CDK2 STRUCTURE MODEL 2.15 42.93 15562 779 99.693 0.244 0.2416 0.2581 0.3001 RANDOM 39.933
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] -0.073 2.66 -2.587
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.297 r_dihedral_angle_4_deg 22.593 r_dihedral_angle_3_deg 16.179 r_dihedral_angle_1_deg 6.473 r_scangle_it 2.119 r_angle_refined_deg 1.427 r_scbond_it 1.332 r_mcangle_it 1.089 r_angle_other_deg 0.914 r_mcbond_it 0.605
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.297 r_dihedral_angle_4_deg 22.593 r_dihedral_angle_3_deg 16.179 r_dihedral_angle_1_deg 6.473 r_scangle_it 2.119 r_angle_refined_deg 1.427 r_scbond_it 1.332 r_mcangle_it 1.089 r_angle_other_deg 0.914 r_mcbond_it 0.605 r_symmetry_hbond_refined 0.235 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.19 r_nbd_other 0.181 r_nbtor_refined 0.179 r_symmetry_vdw_other 0.176 r_symmetry_vdw_refined 0.118 r_nbtor_other 0.088 r_chiral_restr 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.001 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 2209 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling AMoRE phasing