Experiment: 6AB9

The crystal structure of the relaxed state of Nonlabens marinus Rhodopsin 3

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5G28

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	6	293	30% polyethylene glycol dimethyl ether 500, 0.1 M sodium chloride, 0.1 M MES (pH 6.0)

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.634	α = 90
b = 49.22	β = 110.02
c = 69.327	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	PIXEL	DECTRIS PILATUS3 S 6M		2018-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.0	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.75	33.636	98.7	0.061	1	20.5	3.2		32559			22

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78

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	5G28	1.75	33.636	1.38	32542	1620	98.62	0.1766	0.1753	0.1764	0.2037	0.2051

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	13.915
f_angle_d	1.004
f_chiral_restr	0.135
f_plane_restr	0.004
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2072
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	121

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement