4RET

Crystal structure of the Na,K-ATPase E2P-digoxin complex with bound magnesium


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 292.0
Details 16% PEG2000 MME, 10% glycerol, 200 mM magnesium chloride, 100 mM MES-NMDG, pH 6.2, 25 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 118.24 α = 90
b = 118.35 β = 90
c = 494.09 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2013-10-12
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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
3.89 50 68.6 -- -- -- 5.6 64928 44534 1.76 1.76 149.72
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
3.89 3.99 3.8 -- -- 1.76 4.8 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 4.0 49.409 -- 2.0 43077 43077 2144 72.21 -- 0.2229 0.2213 0.2531 --
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 4.0003 4.0933 -- 19 404 0.3009 0.3431 -- 11.0
X Ray Diffraction 4.0933 4.1956 -- 36 703 0.2867 0.3751 -- 19.0
X Ray Diffraction 4.1956 4.309 -- 49 1197 0.2756 0.3545 -- 32.0
X Ray Diffraction 4.309 4.4357 -- 82 1665 0.2584 0.2982 -- 45.0
X Ray Diffraction 4.4357 4.5788 -- 113 2101 0.2538 0.3034 -- 56.0
X Ray Diffraction 4.5788 4.7423 -- 138 2502 0.2371 0.2693 -- 67.0
X Ray Diffraction 4.7423 4.932 -- 150 2884 0.2424 0.2606 -- 77.0
X Ray Diffraction 4.932 5.1563 -- 184 3269 0.2436 0.2705 -- 88.0
X Ray Diffraction 5.1563 5.4278 -- 171 3645 0.243 0.3005 -- 96.0
X Ray Diffraction 5.4278 5.7674 -- 185 3632 0.2511 0.2832 -- 96.0
X Ray Diffraction 5.7674 6.2119 -- 215 3665 0.2444 0.302 -- 97.0
X Ray Diffraction 6.2119 6.8356 -- 195 3681 0.2183 0.2663 -- 98.0
X Ray Diffraction 6.8356 7.8213 -- 189 3778 0.1983 0.2352 -- 98.0
X Ray Diffraction 7.8213 9.8412 -- 201 3860 0.1668 0.2004 -- 99.0
X Ray Diffraction 9.8412 49.4127 -- 217 3947 0.2261 0.2327 -- 98.0
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.128
f_chiral_restr 0.039
f_plane_restr 0.004
f_bond_d 0.009
f_dihedral_angle_d 15.335
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 20704
Nucleic Acid Atoms 0
Heterogen Atoms 413
Solvent Atoms 6

Software

Software
Software Name Purpose
XDS data scaling
PHASER phasing
PHENIX refinement version: (phenix.refine: dev_1593)
XDS data reduction
Diffraction data scaling version: anisotropy server