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Functional construct of the Eukaryotic elongation factor 2 kinase bound to an ATP-competitive inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7SHQ Only residues 80-148 were used for chain B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.2 295.15 Cocktail:16.55% PEG-3350, 200 mM NaF, 100 mM BisTris-Propane
Protein sol: 10.3 mg/mL 20 mM Tris pH 7.5, 100 mM NaCl, 3 mM CaCl2, 1mM TCEP, 0.3 mM ADP, 0.3 m Inhibitor , 0.7 % DMSO
2protein/1cocktail (0.2 ul total)
Crystal Properties Matthews coefficient Solvent content 2.64 53.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.544 α = 90 b = 60.684 β = 111.1 c = 88.704 γ = 90
Symmetry Space Group P 1 21 1
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 Horizontal pre-focus bimorph mirror & KB bimorph mirrors 2022-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97934 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.009 75.133 100 0.2073 0.2274 0.0924 0.985 4.97 5.99 53518
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.009 2.044 100 3.6511 3.9851 1.5825 0.311 0.68 6.13 2638
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 FREE R-VALUE 7SHQ 2.12 47.73 1.34 45318 2303 99.14 0.2086 0.2071 0.2071 0.2376 0.2409 48.69
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 5.9337 f_angle_d 0.5148 f_chiral_restr 0.0376 f_plane_restr 0.0034 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4215 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 51
Software Software Software Name Purpose PHENIX refinement autoPROC data processing Aimless data scaling TRUNCATE data processing XDS data reduction PHASER phasing Coot model building