6XYN

Crystal structure of a proteolytic fragment of NarQ comprising sensor and TM domains

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE		295	1 M KH2PO4/Na2HPO4 pH 5.2 and 5 mM NaNO3

Crystal Properties
Matthews coefficient	Solvent content
3.36	63.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.283	α = 90
b = 51.283	β = 90
c = 182.988	γ = 90

Symmetry
Space Group	I 4

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 PILATUS 6M-F		2015-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9724	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	49.38	97.8	0.064	0.073	0.035	0.999	13.2	4.3		10245

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	2.38	99.8		0.554	0.632	0.299	0.772		4.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5IJI	2.3	49.38	9733	512	97.71	0.2507	0.249	0.2848	RANDOM	70.04

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]
-0.49			-0.49		0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.774
r_dihedral_angle_4_deg	13.389
r_dihedral_angle_3_deg	12.123
r_dihedral_angle_1_deg	3.384
r_angle_refined_deg	0.677
r_angle_other_deg	0.521
r_chiral_restr	0.04
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.774
r_dihedral_angle_4_deg	13.389
r_dihedral_angle_3_deg	12.123
r_dihedral_angle_1_deg	3.384
r_angle_refined_deg	0.677
r_angle_other_deg	0.521
r_chiral_restr	0.04
r_bond_refined_d	0.004
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	1243
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
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 R01GM133198.