6GYH

Crystal structure of the light-driven proton pump Coccomyxa subellipsoidea Rhodopsin CsR

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	1-(9Z-octadecenoyl)-rac-glycerol, 10 % cholesterol, 42 % v/v polyethylene glycol 400; 100 mM MES; pH 6.5, 150 mM sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.078	α = 90
b = 78.078	β = 90
c = 143.951	γ = 120

Symmetry
Space Group	H 3

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 2M		2016-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8729	ESRF	ID23-2

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	2	32.91	100	0.066	0.997	6.8	4.4		22100

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	2	2.05	100		0.901	0.357	0.8	4.6

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3AM6	2	32.91	20932	1155	99.98	0.19398	0.19231	0.22493	RANDOM	43.432

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]
0.59	0.29		0.59		-1.9

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	42.288
r_dihedral_angle_2_deg	37.1
r_dihedral_angle_4_deg	13.223
r_dihedral_angle_3_deg	11.955
r_sphericity_bonded	6.341
r_dihedral_angle_1_deg	5.159
r_long_range_B_refined	2.983
r_long_range_B_other	2.969
r_mcangle_it	2.764
r_mcangle_other	2.764
r_angle_other_deg	2.297
r_scangle_other	2.284
r_mcbond_it	2.21
r_mcbond_other	2.181
r_scbond_it	2.011
r_scbond_other	1.982
r_angle_refined_deg	1.973
r_rigid_bond_restr	1.291
r_chiral_restr	0.193
r_bond_refined_d	0.013
r_bond_other_d	0.009
r_gen_planes_refined	0.005
r_gen_planes_other	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1706
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	118

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing