8QLF

Crystal structure of the light-driven sodium pump ErNaR in the monomeric form at pH 8.8

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	8.8	293	0.1M sodium acetate, 10% PEG550MME, soaked in 0.1M Tris-HCl pH 8.8, 10% PEG550MME prior to crystal harvesting.

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.382	α = 90
b = 53.382	β = 90
c = 364.842	γ = 120

Symmetry
Space Group	P 61 2 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 EIGER X 16M		2022-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.976	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	1.707	46.23	94.66	0.038	0.9991	13.769	37.6		26414

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	1.707	1.875			0.518	0.7444	1.59

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.71	20	25066	1304	75.49	0.18443	0.18271	0.21819	RANDOM	29.838

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]
0.27	0.14		0.27		-0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.68
r_dihedral_angle_3_deg	13.515
r_dihedral_angle_4_deg	13.013
r_long_range_B_other	6.728
r_long_range_B_refined	6.722
r_scangle_other	5.449
r_dihedral_angle_1_deg	5.135
r_mcangle_other	3.808
r_mcangle_it	3.804
r_scbond_other	3.681
r_scbond_it	3.676
r_mcbond_it	2.828
r_mcbond_other	2.812
r_angle_other_deg	1.113
r_angle_refined_deg	1.046
r_chiral_restr	0.049
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_gen_planes_other	0.001
r_bond_other_d
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2168
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	214

Software

Software
Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
XDS	data reduction
STARANISO	data scaling