6YBY | pdb_00006yby

Crystal structure of the D116N mutant of the light-driven sodium pump KR2 in the monomeric form, pH 4.6

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	4.6	293	2 M NaMal pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.887	α = 90
b = 83.601	β = 90
c = 233.83	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 S 6M		2018-08-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.978	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	1.8	40.81	99.8	0.046	0.05	0.02	0.999	16.2	6.6		37771

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	1.8	1.84	99.7		1	1.081	0.406	0.905		7

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	1.8	19.83	35822	1921	99.65	0.2023	0.2013	0.21	0.22	0.23	RANDOM	43.739

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]
0.25			0.41		-0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.118
r_dihedral_angle_4_deg	27.804
r_dihedral_angle_3_deg	12.954
r_dihedral_angle_1_deg	4.729
r_angle_other_deg	1.097
r_angle_refined_deg	1.068
r_chiral_restr	0.053
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.118
r_dihedral_angle_4_deg	27.804
r_dihedral_angle_3_deg	12.954
r_dihedral_angle_1_deg	4.729
r_angle_other_deg	1.097
r_angle_refined_deg	1.068
r_chiral_restr	0.053
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2147
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	269

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.