5KAI | pdb_00005kai

NH3-bound RT XFEL structure of Photosystem II 500 ms after the 2nd illumination (2F) at 2.8 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
3.71	66.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.911	α = 90
b = 224.268	β = 90
c = 330.996	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	1.7492	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	2.8	43.569812	99	0.524	11.62	13.7		213400			60.4069710515

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	2.8	2.8483	95.96		1.935	4.17

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	2.80000914773	43.5698116774	1.32517238381	211388	1792	98.0418347943	0.250157325862	0.249733595601	0.25	0.299747309097	0.3	Random selection w.r.t. complete reflections to 2 Angstroms	56.5229924032

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	21.0338406301
f_angle_d	0.59701867629
f_chiral_restr	0.0401636589989
f_plane_restr	0.00478620789921
f_bond_d	0.00308519133984

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	41698
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	8476

Software

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

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.