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Functional construct of the Eukaryotic elongation factor 2 kinase bound to Calmodulin, ADP and to the A-484954 inhibitor and showing two conformations for the 498-520 loop
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7SHQ Only residues 80-148 were used for Calmodulin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 295.15 Cocktail:16.55% PEG-3350, 0.2 M NaF, 100 mM BisTris-Propane
Protein solution: 10.3 mg/mL 20 mM Tris pH 7.5, 100 mM NaCl, 3 mM CaCl2, 1mM TCEP, 1.5 m Inhibitor , 3.1 % DMSO
2protein/1cocktail (0.2 ul total)
Crystal Properties Matthews coefficient Solvent content 2.68 53.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.909 α = 90 b = 61.041 β = 111.26 c = 88.958 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 2.12 82.906 92 0.1221 0.1367 0.0603 0.996 5.89 4.93 30789
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) 2.124 2.338 53.4 0.8888 1.0091 0.4736 0.567 1.46 4.45 1539
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 45.94 1.36 30782 1534 67.1 0.183 0.181 0.1812 0.225 0.2251 42.27
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 5.304 f_angle_d 0.518 f_chiral_restr 0.039 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4304 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 51
Software Software Software Name Purpose PHENIX refinement autoPROC data processing XDS data reduction Aimless data scaling PHASER phasing Coot model building