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Cdk2(F80C) with Covalent Adduct TK37 at F80C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EK3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Protein: 8 mg/mL in pH 6.2 phosphate buffer
Resovoir: 8-12% PEG3350, HEPES 0.1 M (pH 7.5-8.5)
1:1
Crystal Properties Matthews coefficient Solvent content 1.99 38.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.34 α = 90 b = 71.24 β = 90 c = 71.87 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 ADSC QUANTUM 315 2018-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9763 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.66 36.71 99.57 0.06219 0.995 7.81 2 32900 24.6
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 1.66 1.719 0.488
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4EK3 1.66 36.71 32893 99.57 0.2212 0.2214 0.2685 0.2673 35.84
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 23.9157 f_angle_d 0.9722 f_chiral_restr 0.0557 f_bond_d 0.0072 f_plane_restr 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2237 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 22
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing