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Crystal structure of the Na,K-ATPase E2P-bufalin complex with bound potassium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HYT PDB ENTRY 4HYT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 292 17% PEG2000 MME, 10% glycerol, 220 mM magnesium chloride, 100 mM potassium chloride, 100 mM MES-KOH, pH 6.2, 5% MPD, 6% Jeffamine M-600, 0.02% beta-DDM, 2 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 3.81 67.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.91 α = 90 b = 240.27 β = 102.28 c = 152.7 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 PSI PILATUS 6M 2009-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.408 55 50.2 10.4 5.9 63228 31754 2.24 2.24 80.97
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.408 3.5 1.4 2.24 5.7
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 4HYT 3.408 49.903 2 31546 31546 1623 49.94 0.247 0.2447 0.2882 0.239 RANDOM
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 15.071 f_angle_d 1.225 f_chiral_restr 0.076 f_bond_d 0.011 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20654 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 227
Software Software Software Name Purpose XDS data scaling PHASER phasing PHENIX refinement XDS data reduction Diffraction data scaling