4L35

Crystal structure of cruxrhodopsin-3 at pH5 from Haloarcula vallismortis at 2.1 angstrom resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JR8	PDB ENTRY 4JR8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	288	2.5M ammonium sulfate, 0.1M Na-citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.01	α = 90
b = 106.01	β = 90
c = 55.44	γ = 120

Symmetry
Space Group	P 3 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 315		2013-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0	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	2.1	47.46	93.1	0.079	0.079	20.8	7.3	21114	19657			24.6

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	2.1	2.21	96.9		0.494	4.6	7.4	2982

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4JR8	2.1	15	21193	19593	1929	92.5	0.2314	0.2314	0.2314	0.2522	RANDOM	31.415

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]
3.773			3.773		-7.545

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	18.61611
c_angle_deg	1.15176
c_improper_angle_d	0.77779
c_bond_d	0.005642

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1862
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	57

Software

Software
Software Name	Purpose
ADSC	data collection
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

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.