Experiment: 5KAF

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4UB6	PSII monomer composed of 4UB6 monomer and additional chain from 4PJ0
experimental model	PDB	4PJ0	PSII monomer composed of 4UB6 monomer and additional chain from 4PJ0

Crystallization

Crystalization Experiments
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.

Crystal Properties
Matthews coefficient	Solvent content
3.69	66.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.731	α = 90
b = 223.815	β = 90
c = 330.818	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	293	PIXEL	CS-PAD CXI-1	1 micron KB mirror	2014-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE CXI	1.7493	SLAC LCLS	CXI

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	3	43.12381	97.3	0.532	10.505	8.48		170444			61.0479099572

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.0517	88.8		2.257	2.91

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PSII monomer composed of 4UB6 monomer and additional chain from 4PJ0	3.00000997771	43.1230807017	1.32591484095	168044	1446	96.0284352606	0.264021318029	0.263691700807	0.2659	0.303040832505	0.3035	Random selection w.r.t. complete reflections to 2 Angstroms	47.3328786731

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.9369033292
f_angle_d	0.487434134126
f_chiral_restr	0.0370617522078
f_plane_restr	0.00411381903435
f_bond_d	0.00191204375673

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	41612
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	8423

Software

Software
Software Name	Purpose
PHENIX	refinement
cctbx.xfel	data reduction
cctbx.prime	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction