Experiment: 7M78

Room Temperature XFEL Crystallography reveals asymmetry in the vicinity of the two phylloquinones in Photosystem I

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JB0	PDB entry 1JB0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		298	5 mM MES, pH 6.0, 12 mM sodium sulfate, 0.2% beta-dodecyl maltoside

Crystal Properties
Matthews coefficient	Solvent content
7.41	83.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 284.864	α = 90
b = 284.864	β = 90
c = 166.177	γ = 120

Symmetry
Space Group	P 63

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	MPCCD		2019-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL2	1.181	SACLA	BL2

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	3	31.63	99.9	0.893	3.2	282.5		152883			41.08

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	3	3.05			0.098

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	PDB entry 1JB0	3	31.63	1.34	152693	1995	99.88	0.3339	0.3337	0.3345	0.3498	0.3499	42.1

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	18.0419
f_angle_d	0.6601
f_chiral_restr	0.0417
f_plane_restr	0.0053
f_bond_d	0.0029

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17524
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms	6869

Software

Software
Software Name	Purpose
cctbx.xfel	data reduction
PHENIX	refinement