9VJ2

Crystal structure of palytoxin-bound Na+,K+-ATPase in the E2P state

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SPRING-8 BEAMLINE BL41XU
Synchrotron site	SPring-8
Beamline	BL41XU
Temperature [K]	100
Detector technology	PIXEL
Collection date	2015-07-18
Detector	DECTRIS PILATUS 6M
Wavelength(s)	1
Spacegroup name	P 43 21 2
Unit cell lengths	85.022, 85.022, 646.129
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	10.000 - 3.790
R-factor	0.2293
Rwork	0.227
R-free	0.27570
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.005
RMSD bond angle	0.837
Data reduction software	HKL-2000
Data scaling software	HKL-2000
Phasing software	PHASER
Refinement software	PHENIX (1.21.2_5419)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	50.000	4.250
High resolution limit [Å]	3.790	3.790
Rmerge	0.259	1.307
Number of reflections	11915	794
<I/σ(I)>	8.6	1.8
Completeness [%]	47.6	11.1
Redundancy	12.7	7.2
CC(1/2)	0.987	0.557

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	6.2	288	140 mM MgCl2, 25 mM NaCl, 15.4% (w/v) PEG2000MME, 7% (w/v) glycerol, 0.4 mM palytoxin, 1 mM BeCl3, 3.5 mM NaF, 5 mM GSH, 0.1 mM DTT and 1 mg/ml butylhydroxytoluen, 100 mM MES