Experiment: 8RSO

Crystal structure of marine actinobacteria clade rhodopsin (MAR) in the ground state

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	8.8	293	3.0 M Ammonium Phosphate buffer, pH 8.8

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.71	α = 64.09
b = 55.85	β = 81.52
c = 56.64	γ = 85.29

Symmetry
Space Group	P 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 EIGER2 X 16M		2022-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9537	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.24	47.23	86.6	0.037	0.996	9.6	3.6		92902			30.08

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.24	1.36	35.3		0.67	0.352	1.3	2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.25	47.23	1.96	92892	4304	74.78	0.1527	0.1515	0.1521	0.1768	0.176	25.57

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	13.7702
f_angle_d	1.1233
f_chiral_restr	0.0776
f_bond_d	0.0102
f_plane_restr	0.0089

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3342
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms	285

Software

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