5TIS | pdb_00005tis

Room temperature XFEL structure of the native, doubly-illuminated photosystem II complex

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	6.5	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
3.46	64.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.87	α = 90
b = 223.14	β = 90
c = 310.71	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	CCD	RAYONIX MX170-HS	Compound refractive lenses	2015-11-18	M	SINGLE WAVELENGTH
2	1	x-ray	293	CCD	RAYONIX MX170-HS	Compound refractive lenses	2016-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE XPP	1.3051	SLAC LCLS	XPP
2	FREE ELECTRON LASER	SLAC LCLS BEAMLINE MFX	1.3051	SLAC LCLS	MFX

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	2.25	44.28	99.98	0.974	19.834	158.47		385545			42.9839105609

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)
	2.25	2.289	99.98		0.018	2.036	10.37

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	5KAI	2.25000371562	44.2766212822	1.32535968968	385545	3426	99.933385519	0.193550152737	0.193214944928	0.19	0.230881600007	0.23	Random selection w.r.t. complete reflections to 2 Angstroms	47.7620084464

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	14.9024531457
f_angle_d	0.503129489462
f_chiral_restr	0.0382482334883
f_bond_d	0.00571882994341
f_plane_restr	0.00393061979526

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	41719
Nucleic Acid Atoms
Solvent Atoms	1179
Heterogen Atoms	8659

Software

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

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.