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Crystal structure of CDK2 liganded with compound WN378
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DK1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 4.5 mg/mL CDK2 crystalized in 50 mM sodium/potassium phosphate, 50 mM HEPES, pH 7.5, 5% v/v PEG3350, soaked overnight in 1 mM WN378 in 50 mM phosphate, 50 mM HEPES Na, 10% v/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.06 40.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.657 α = 90 b = 71.924 β = 90 c = 72.371 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 PIXEL DECTRIS EIGER X 16M 2021-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03317 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.53 43.12 90.25 0.091 0.1 0.996 10.5 5.1 38877 33.14
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.53 1.56 45.87 0.75 0.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4dk1 1.69 43.01 1.36 31807 2072 99.21 0.2312 0.2301 0.2361 0.2623 0.2724 43.4128
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2137 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 27
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction xia2 data reduction PHENIX phasing