5KAF

RT XFEL structure of Photosystem II in the dark state at 3.0 A resolution

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	FREE ELECTRON LASER
Source details	SLAC LCLS BEAMLINE CXI
Synchrotron site	SLAC LCLS
Beamline	CXI
Temperature [K]	293
Detector technology	PIXEL
Collection date	2014-11-28
Detector	CS-PAD CXI-1
Wavelength(s)	1.7493
Spacegroup name	P 21 21 21
Unit cell lengths	117.731, 223.815, 330.818
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	43.123 - 3.000
R-factor	0.264021318029
Rwork	0.264
R-free	0.30304
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	PSII monomer composed of 4UB6 monomer and additional chain from 4PJ0
RMSD bond length	0.002
RMSD bond angle	0.487
Data reduction software	cctbx.xfel
Data scaling software	cctbx.prime
Phasing software	PHASER
Refinement software	PHENIX (dev_2411)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	43.124	43.124	3.052
High resolution limit [Å]	3.000	8.143	3.000
Number of reflections	170444
<I/σ(I)>	10.505	45.59	2.257
Completeness [%]	97.3	99.06	88.8
Redundancy	8.48	30.12	2.91
CC(1/2)	0.532

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	BATCH MODE	7.5	293	Crystal growth was as described in Kern et al. 2005, Biochim. Biophys. Acta-Bioenergetics and Ibrahim et al. 2015, Struct. Dyn. 2 (4), 041705, substituting C12E8 for beta-DM and Betaine for glycerol.