5B0W

Crystal structure of the 11-cis isomer of pharaonis halorhodopsin in the absence of halide ions

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	288	A mixture solution containing 3mg/ml halorhodopsin, 1M ammonium sulfate, 0.1M NaCl, 0.1 M sodium citrate, and 5.7mg/ml nonylglucoside was concentrated by the sitting-drop vapor diffusion method. Before data collection, the crystal was soaked in an alkaline solution containing no halide ions, illuminated with red light, and then soaked in a solution at pH 7.

Crystal Properties
Matthews coefficient	Solvent content
1.61	23.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.32	α = 90
b = 97.93	β = 128.67
c = 101.53	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	RAYONIX MX225HE		2015-06-11	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	1.7	50.7	96.8	0.059	0.059	11.7	3.2		125077	2.5		17.11

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	1.7	1.79	81.8		0.393	2.4	2.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION		FREE R-VALUE	1.7	15	124943	5461	96.7	0.202	0.2154	22.3454

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]
1.568		2.017	0.483		-2.051

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_d	1.45
c_bond_d	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11774
Nucleic Acid Atoms
Solvent Atoms	444
Heterogen Atoms	432

Software

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

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 R01GM133198.