6YC4

Crystal structure of the steady-state activated state of the light-driven sodium pump KR2 in the pentameric form at room temperature, pH 8.0

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6XYT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	8	293	1.2 M NaMal pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
3.64	66.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.189	α = 90
b = 239.861	β = 90
c = 138.456	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	DECTRIS EIGER X 16M		2019-10-14	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)	R Merge I (Observed)	Rrim I (All)	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	2.59	48.81	99.6	0.237	0.252	0.086	0.994	6.7	8.5		69594

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.59	2.65	94.8		2.131	2.27	0.771	0.507		8.6

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	6xyt	2.6	20	65587	3487	99.63	0.1861	0.1847	0.2123	RANDOM	49.282

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]
4.56			-6.08		1.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.042
r_dihedral_angle_3_deg	9.089
r_dihedral_angle_4_deg	6.007
r_dihedral_angle_1_deg	2.18
r_angle_refined_deg	1.077
r_angle_other_deg	1.045
r_chiral_restr	0.038
r_gen_planes_refined	0.002
r_bond_refined_d	0.001
r_bond_other_d

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.042
r_dihedral_angle_3_deg	9.089
r_dihedral_angle_4_deg	6.007
r_dihedral_angle_1_deg	2.18
r_angle_refined_deg	1.077
r_angle_other_deg	1.045
r_chiral_restr	0.038
r_gen_planes_refined	0.002
r_bond_refined_d	0.001
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10769
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms	741

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.