Experiment: 9SOD

Atomic resolution structure of viral channelrhodopsin OLPVR1 in a complex with calcium ion bound at the surface

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9IN7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	8	293	100 mM Tris, 900 mM NaCl, and 24% (w/v) PEG 6000 Soaking in: 100 mM Tris, 900 mM NaCl, 24% (w/v) PEG 6000, and 100 mM CaCl2

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.454	α = 90
b = 115.357	β = 90
c = 53.498	γ = 90

Symmetry
Space Group	P 21 21 2

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		2023-09-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.8856	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	1.45	36.18	86.4	0.029	0.998	11.6	4.8		33974			20.69

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	1.45	1.62	52.5		0.449	0.645	1.6	4.5

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	1.45	35.08	1.36	33960	1684	65.97	0.1701	0.1686	0.1689	0.1974	0.1979	27.92

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	15.2442
f_angle_d	0.7648
f_chiral_restr	0.0688
f_bond_d	0.006
f_plane_restr	0.0045

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1920
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	262

Software

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