8JBL
Crystal structure of Na+,K+-ATPase in the E1.Mg2+ state
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8JBK | deposition ID: D_1300037566 |
Crystallization
Crystalization Experiments | ||||
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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 | |
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Matthews coefficient | Solvent content |
3.46 | 64.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 196.797 | α = 90 |
b = 74.319 | β = 116.289 |
c = 163.553 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 1 | SPring-8 | BL41XU |
Data Collection
Overall | |||||||||||||||||||
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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 | |||||||||||||||||||
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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 | |||||||||||||||||||
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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 | R-Free | 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 | 0.2823 | 90.02 |
Temperature Factor Modeling | ||||||
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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 | |
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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 | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 20765 |
Nucleic Acid Atoms | |
Solvent Atoms | 33 |
Heterogen Atoms | 884 |
Software
Software | |
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Software Name | Purpose |
BSS | data collection |
HKL-2000 | data reduction |
STARANISO | data scaling |
PHASER | phasing |
PHENIX | refinement |