6DHO

RT XFEL structure of the two-flash state of Photosystem II (2F, S3-rich) at 2.07 Angstrom resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5KAF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	6.5	298	0.1 M MES pH 6.5, 0.1 M NH4Cl, 35% (w/v) PEG 5000

Crystal Properties
Matthews coefficient	Solvent content
3.4	63.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.011	α = 90
b = 221.542	β = 90
c = 308.346	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	298	CCD	RAYONIX MX170-HS	Compound refractive lenses	2016-07-14	M	SINGLE WAVELENGTH
3	1	x-ray	298	CCD	RAYONIX MX170-HS	Compound refractive lenses	2017-07-13	M	SINGLE WAVELENGTH
2	1	x-ray	298	CCD	RAYONIX MX170-HS	Compound refractive lenses	2016-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE MFX	1.305	SLAC LCLS	MFX
3	FREE ELECTRON LASER	SLAC LCLS BEAMLINE MFX	1.305	SLAC LCLS	MFX
2	FREE ELECTRON LASER	SLAC LCLS BEAMLINE MFX	1.305	SLAC LCLS	MFX

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		fixed target

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	40	10	3	9.515

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	2.07	30.58	99.96	0.982	15.463	207.28		483509

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.07	2.106	99.98		0.021	0.582	13.75

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5KAF	2.07	30.578	1.33	482673	4285	99.82	0.185	0.1844	0.2475	46.7274

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	41576
Nucleic Acid Atoms
Solvent Atoms	1886
Heterogen Atoms	19205

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.