Experiment: 4TNJ

RT XFEL structure of Photosystem II 500 ms after the 2nd illumination (2F) at 4.5 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BZ1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	7	298	4% PEG2000, 5 mM calcium chloride, 100 mM PIPES, pH 7.0, BATCH, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.66	66.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.298	α = 90
b = 228.713	β = 90
c = 307.976	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	PIXEL	CS-PAD detector	KB mirrors	2013-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE CXI	1.77	SLAC LCLS	CXI

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	4.5	72.97	99.5	52.1	131.4		52965			152.708766903

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	4.5	4.66	95.8		3.7	7.8

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3BZ1	4.5	72.97	1.36387170175	103594	5072	96.7535257308	0.276062023076	0.275634173434	0.2799	0.284372171937	0.2877	174.041622556

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	18.6584677639
f_angle_d	0.756574072852
f_chiral_restr	0.0294451364392
f_bond_d	0.00480991479501
f_plane_restr	0.00397383103447

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	41052
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	9192

Software

Software
Software Name	Purpose
PHENIX	refinement
cctbx.xfel	data reduction