5ETZ

Structure of the all-trans isomer of pharaonis halorhodopsin in the absence of halide ions

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	288	The crystal was prepared by the membrane fusion method. A mixture solution containing 3 mg/ml halorhodopsin, 9 mg/ml nonylglucoside, 1 M ammonium sulfate, 0.1 M sodium azide was concentrated by the sitting-drop vapor diffusion method. The crystal soaking in a halide-ion-free solution was performed under dim red light, and then the crystal was rapidly cooled with liquid propane at 87 K.

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.4	α = 90
b = 97.77	β = 128.81
c = 101.62	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2015-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1	SPring-8	BL38B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (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	1.8	50.77	91.3	0.065	0.065	12.7	3.5	99234	99234		2.5	16

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	60.9		0.405	2.7	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3qbg	1.8	15	99008	5001	91.2	0.2185	0.2357	Random selection

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]
0.47		0.919	2.01		-2.48

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5900
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms	343

Software

Software
Software Name	Purpose
CNS	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
XTALVIEW	model building

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.