6RF7 | pdb_00006rf7

Crystal structure of the light-driven sodium pump KR2 in the monomeric form, pH 8.9

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE		293	2.0 M Sodium Malonate, pH 4.3

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.598	α = 90
b = 82.248	β = 90
c = 234.183	γ = 90

Symmetry
Space Group	I 2 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 PILATUS3 6M		2016-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.000	ESRF	ID23-1

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	2.5	40.7	99.6	0.107	0.12	0.053	0.999	9.4	4.8		14043

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	2.5	2.6	99.9		1.537	1.716	0.75	0.56		5

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	4XTL	2.6	20	11878	598	99.01	0.224	0.2215	0.24	0.2711	0.28	RANDOM	61.589

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]
2.51			4.19		-6.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.367
r_dihedral_angle_4_deg	27.962
r_dihedral_angle_3_deg	17.002
r_dihedral_angle_1_deg	5.996
r_angle_other_deg	0.748
r_angle_refined_deg	0.504
r_chiral_restr	0.026
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.367
r_dihedral_angle_4_deg	27.962
r_dihedral_angle_3_deg	17.002
r_dihedral_angle_1_deg	5.996
r_angle_other_deg	0.748
r_angle_refined_deg	0.504
r_chiral_restr	0.026
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2124
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms	54

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.