6XYT | pdb_00006xyt

Crystal structure of the O-state 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	6REW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE		293	0.7 M Sodium Malonate pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
3.43	64.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.157	α = 90
b = 240.629	β = 90
c = 135.039	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		2019-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	1.00	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	2.1	48.06	99.8	0.078	0.081	0.022	0.999	20.1	13.8		123865

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	2.1	2.14	99.9		2.76	2.863	0.757	0.56		14

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6REW	2.1	20	117421	6234	99.58	0.1798	0.1789	0.19	0.1974	0.21	RANDOM	57.586

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]
5			-5.51		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.934
r_dihedral_angle_4_deg	14.291
r_dihedral_angle_3_deg	13.024
r_dihedral_angle_1_deg	4.933
r_angle_other_deg	1.108
r_angle_refined_deg	1.052
r_chiral_restr	0.044
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.934
r_dihedral_angle_4_deg	14.291
r_dihedral_angle_3_deg	13.024
r_dihedral_angle_1_deg	4.933
r_angle_other_deg	1.108
r_angle_refined_deg	1.052
r_chiral_restr	0.044
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10865
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms	1185

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.