7RF8

RT XFEL structure of the two-flash state of Photosystem II (2F, S3-rich) at 2.09 Angstrom resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6DHE

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
3.16	61.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.958	α = 90
b = 221.646	β = 90
c = 307.786	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 MX340-HS		2018-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE CXI	1.30192	SLAC LCLS	CXI

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	Drop-on-Tape	injection

Injection
Diffraction ID	Description	Flow Rate	Injector Diameter	Injection Power	Injector Nozzle	Filter Size	Carrier Solvent
1	Acoustic Droplet Ejection			Acoustic Wave

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	40	20	9	9.52

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Total Frames
1

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	2.09	33.65	99.8	0.979	12.8	81		468019			37.65

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	2.09	2.21	97.42		0.044	0.6

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	FREE R-VALUE	6DHE	2.09	33.65	1.33	465551	4128	99.26	0.1816	0.181	0.2388	45.46

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	18.0417
f_angle_d	1.462
f_chiral_restr	0.0605
f_bond_d	0.0145
f_plane_restr	0.0107

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	41525
Nucleic Acid Atoms
Solvent Atoms	1904
Heterogen Atoms	8582

Software

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

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.