Experiment: 9SOF

Atomic resolution structure of viral channelrhodopsin OLPVR1 in a complex with calcium ion bound inside the channel

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: 100 mM Tris, 900 mM NaCl, 24% (w/v) PEG 6000, and 10 mM CaCl2

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.392	α = 90
b = 115.449	β = 90
c = 53.418	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 CdTe 16M		2022-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9755	PETRA III, EMBL c/o DESY	P14 (MX2)

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	1.41	43.05	95.2	0.016	0.999	19	13		51500			22.01

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	1.41	1.46	66		0.919	0.272	0.8	9.2

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	1.41	43.05	1.33	51341	2589	90.75	0.1781	0.1767	0.1768	0.2043	0.2048	28.65

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	15.3582
f_angle_d	1.0746
f_chiral_restr	0.0842
f_bond_d	0.01
f_plane_restr	0.0069

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1909
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms	263

Software

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