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Crystal structure of Na+,K+-ATPase in the E1.Mg2+ state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8JBK deposition ID: D_1300037566
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 283 285 mM NaCl, 25 mM MgCl2, 15.4% (w/v) PEG2000MME, 7% (w/v) glycerol, 5 mM GSH, 0.1 mM DTT and 1 mg/ml butylhydroxytoluen, 100 mM MES
Crystal Properties Matthews coefficient Solvent content 3.46 64.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 196.797 α = 90 b = 74.319 β = 116.289 c = 163.553 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 2020-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1 SPring-8 BL41XU
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 3 30 53.7 0.174 0.973 7.03 3.5 46000 82.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.1 4.1 0.603 0.283 1.34 1.6
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 8JBK 3 11.99 1.36 44648 2243 53.05 0.2356 0.233 0.2384 0.2823 0.2884 90.02
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 17.8208 f_angle_d 0.7767 f_chiral_restr 0.047 f_plane_restr 0.0054 f_bond_d 0.0038
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20765 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 884
Software Software Software Name Purpose BSS data collection HKL-2000 data reduction STARANISO data scaling PHASER phasing PHENIX refinement