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CDK2 in complex with NSC 134199
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PXZ PDB ENTRY 3PXZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 5 mg/mL CDK2 protein, 5% v/v PEG3350, 50 mM HEPES/NaOH, pH 7.5, 50 mM sodium/potassium phosphate, pH 7.5, 10 mM NSC134199 soak, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.93 36.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.42 α = 90 b = 70.39 β = 90 c = 71.46 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 CCD RIGAKU SATURN 944+ 2012-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 20 99.9 0.07 0.065 21 7 18753 -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 2.1 99.9 0.359 0.33 6.4 7
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 3PXZ 2 18.505 1.99 18750 937 99.89 0.2152 0.2111 0.2509 0.2435
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] -0.9988 5.3747 -3.5726
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.797 f_angle_d 1.748 f_chiral_restr 0.086 f_bond_d 0.014 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2366 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 24
Software Software Software Name Purpose StructureStudio data collection PHENIX model building PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing