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Beryllium fluoride form of the Na+,K+-ATPase (E2-BeFx)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7D91
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 288.15 Protein sample was mixed in a 1:1 ratio with reservoir solution containing 16.5 % (wt/vol) polyethylene glycol 2000 monomethyl ether (PEG 2000 MME), 10 % (vol/vol) glycerol, 175 mM MgCl2, 150 mM NaCl, 20 mM HEPES/MES pH 6.2 and 2 mM DTT. The crystals were dehydrated overnight at 4C against a 30 % PEG 2000 MME reservoir solution before flash-cooling.
Crystal Properties Matthews coefficient Solvent content 5.53 77.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.47 α = 90 b = 118.08 β = 90 c = 494.66 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 PIXEL DECTRIS PILATUS3 6M 2015-10-29 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS PILATUS 2M 2015-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 1 PETRA III, EMBL c/o DESY P14 (MX2) 2 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 4.05 29.67 99.5 0.99 6.4 26.2 57347 147.73
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 4.05 4.2 99.6 0.263 0.7
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 THROUGHOUT 7d91 4.05 29.67 1.35 39148 1928 68.87 0.2483 0.2465 0.2499 0.2811 0.2837 188.1761
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20734 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 274
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing