6YBZ

Crystal structure of the D116N mutant of the light-driven sodium pump KR2 in the pentameric form, pH 8.0

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XTO

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
3.47	64.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.343	α = 90
b = 240.477	β = 90
c = 135.415	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	100	PIXEL	DECTRIS EIGER X 16M		2018-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.978	ESRF	ID29

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	2.35	48.13	99.9	0.11	0.119	0.045	0.999	11.3	6.9		89161

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	2.35	2.39	99.9		1.925	2.09	0.808	0.787		6.6

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	4xto	2.35	20	84508	4459	99.73	0.1972	0.1961	0.2175	RANDOM	32.34

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]
4.27			-7.04		2.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.689
r_dihedral_angle_4_deg	20.388
r_dihedral_angle_3_deg	17.799
r_dihedral_angle_1_deg	6.586
r_angle_other_deg	2.375
r_angle_refined_deg	1.088
r_chiral_restr	0.043
r_bond_other_d	0.034
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.689
r_dihedral_angle_4_deg	20.388
r_dihedral_angle_3_deg	17.799
r_dihedral_angle_1_deg	6.586
r_angle_other_deg	2.375
r_angle_refined_deg	1.088
r_chiral_restr	0.043
r_bond_other_d	0.034
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10737
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	445

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
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.