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Crystal structure of CDK2 in complex with inhibitor ICEC0942
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NS9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 277 0.1M AMMONIUM ACETATE, PH 7.8, 6% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.02 39.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.65 α = 90 b = 70.77 β = 90 c = 72.27 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 944+ 2011-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54187
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 1.94 50.56 96.3 0.027 21 3.2 20059
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 1.94 2.05 88.3 0.074 9.2 2.8
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 3NS9 1.94 50.56 19012 1018 95.87 0.18416 0.18108 0.1845 0.24104 0.1897 RANDOM 19.233
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] -0.25 0.29 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.867 r_dihedral_angle_4_deg 17.541 r_dihedral_angle_3_deg 16.588 r_dihedral_angle_1_deg 5.978 r_scangle_it 4.918 r_scbond_it 3.13 r_mcangle_it 2.084 r_angle_refined_deg 2.013 r_mcbond_it 1.221 r_chiral_restr 0.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.867 r_dihedral_angle_4_deg 17.541 r_dihedral_angle_3_deg 16.588 r_dihedral_angle_1_deg 5.978 r_scangle_it 4.918 r_scbond_it 3.13 r_mcangle_it 2.084 r_angle_refined_deg 2.013 r_mcbond_it 1.221 r_chiral_restr 0.155 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_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 2309 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALEPACK data scaling MOLREP phasing