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Crystal Structure of CDK2 in complex with Macrocyclic Aminopyrimidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DM2 PDB ENTRY 1DM2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.8 pH 7.8
Crystal Properties Matthews coefficient Solvent content 2.07 40.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.936 α = 90 b = 69.934 β = 90 c = 71.687 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 BRUKER MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE MACSCIENCE
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 2.5 71.69 99.9 0.04 21.65 14.31 138956
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 2.5 2.6 99.6 0.19 5.35 11.97
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 1DM2 2.5 50 8682 943 99.8 0.219 0.21 0.2179 0.294 0.2018 RANDOM 19.62
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] 0.33 0.75 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.692 r_dihedral_angle_4_deg 19.566 r_dihedral_angle_3_deg 18.725 r_dihedral_angle_1_deg 6.023 r_scangle_it 3.766 r_scbond_it 2.679 r_mcangle_it 1.859 r_angle_refined_deg 1.413 r_mcbond_it 1.044 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.692 r_dihedral_angle_4_deg 19.566 r_dihedral_angle_3_deg 18.725 r_dihedral_angle_1_deg 6.023 r_scangle_it 3.766 r_scbond_it 2.679 r_mcangle_it 1.859 r_angle_refined_deg 1.413 r_mcbond_it 1.044 r_nbtor_refined 0.318 r_symmetry_vdw_refined 0.281 r_symmetry_hbond_refined 0.262 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 2219 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling AMoRE phasing