6RF0 | pdb_00006rf0

Crystal structure of the light-driven sodium pump KR2 in the pentameric "dry" form

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		293	3.4 M Sodium Malonate pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.184	α = 90
b = 239.719	β = 90
c = 131.909	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 4M		2017-10-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.976	ESRF	ID30B

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	3	47.28	99.9	0.304	0.33	0.127	0.989	5.7	6.6		41018

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	3	3.12	100		1.475	1.601	0.618	0.662		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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4XTO	3	47.32	38937	2059	99.92	0.2184	0.2166	0.23	0.2519	0.26	RANDOM	43.925

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]
5.3			-6.49		1.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.261
r_dihedral_angle_4_deg	26.713
r_dihedral_angle_3_deg	19.243
r_dihedral_angle_1_deg	7.637
r_angle_other_deg	0.766
r_angle_refined_deg	0.59
r_chiral_restr	0.028
r_bond_refined_d	0.003
r_gen_planes_refined	0.002
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.261
r_dihedral_angle_4_deg	26.713
r_dihedral_angle_3_deg	19.243
r_dihedral_angle_1_deg	7.637
r_angle_other_deg	0.766
r_angle_refined_deg	0.59
r_chiral_restr	0.028
r_bond_refined_d	0.003
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10841
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	206

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.