6RF5 | pdb_00006rf5

Crystal structure of the light-driven sodium pump KR2 in the monomeric form, pH 6.0

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
3.12	60.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.334	α = 90
b = 81.246	β = 90
c = 233.359	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	2.3	40.62	99.7	0.105	0.116	0.049	0.997	10.4	5.4		17576

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	2.3	2.39	99.5		1.058	1.177	0.506	0.683		5.2

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	2.3	20	16711	831	99.31	0.2047	0.202	0.22	0.2585	0.26	RANDOM	43.942

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]
4.53			0.14		-4.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.858
r_dihedral_angle_4_deg	20.175
r_dihedral_angle_3_deg	15.641
r_dihedral_angle_1_deg	7.085
r_angle_other_deg	0.725
r_angle_refined_deg	0.584
r_chiral_restr	0.034
r_bond_refined_d	0.003
r_gen_planes_refined	0.002
r_gen_planes_other	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.858
r_dihedral_angle_4_deg	20.175
r_dihedral_angle_3_deg	15.641
r_dihedral_angle_1_deg	7.085
r_angle_other_deg	0.725
r_angle_refined_deg	0.584
r_chiral_restr	0.034
r_bond_refined_d	0.003
r_gen_planes_refined	0.002
r_gen_planes_other	0.001
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2134
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	276

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.