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CDK2 in complex with inhibitor YL5-083
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PXR PDB ENTRY 3PXR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 5 mg/mL CDK2 protein, 1.5 mM YL5-83, 5 % (v/v) PEG 3350, 50 mM HEPES/NaOH (pH 7.5), 50 mM phosphate (Na/K, pH 7.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.03 39.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.95 α = 90 b = 72.02 β = 90 c = 72.37 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 93 IMAGE PLATE RIGAKU RAXIS HTC MIRRORS 2011-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.1 20 99.8 0.075 0.071 21 6.9 16682 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 100 0.238 0.297 7 6.9
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 3PXR 2.1 18.744 2 16682 835 99.97 0.1796 0.1756 0.2336 0.2274
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] -2.8221 -4.6729 7.495
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.522 f_angle_d 1.305 f_chiral_restr 0.098 f_bond_d 0.01 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2371 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 29
Software Software Software Name Purpose StructureStudio data collection PHENIX model building PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing