Experiment: 6LM1

The crystal structure of cyanorhodopsin (CyR) N4075R from cyanobacteria Tolypothrix sp. NIES-4075

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1C3W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE		293	0.1M sodium-acetate (pH5.0), 450mM Magnesium nitrate, 28% PEG 500

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.92	α = 90
b = 129.666	β = 90
c = 127.626	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2019-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32XU	1.0	SPring-8	BL32XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.45	49.7	82.6	0.124	0.13	0.038	0.999	10	10.8		129542

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.48	10		0.38974	54.345	0.37738	0.001		1.9

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	THROUGHOUT	1C3W	1.9	45.479	1.35	70556	1090	99.95	0.1658	0.1653	0.1684	0.2041	0.2081	36.8638

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5207
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	641

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing