3SXQ

Structure of a hexameric multiheme c nitrite reductase from the extremophile bacterium Thiolkalivibrio paradoxus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	free-interface-diffusion technique	6.5	278	14 mg/mL protein, 0.02M cobalt chloride, 0.1M MES (pH 6.5), 2.8 M ammonium sulfate, free-interface-diffusion technique, temperature 278.0K

Crystal Properties
Matthews coefficient	Solvent content
5.11	75.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 193.64	α = 90
b = 193.64	β = 90
c = 193.64	γ = 90

Symmetry
Space Group	P 21 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 165 mm		2010-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.800	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.9	29.9	98.9	0.098	9.47		188857	186813			23.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	99.7		0.521	2.24		26633

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	2OT4	1.9	29.9	177340	9466	98.92	0.1394	0.1382	0.16205	RANDOM	15.556

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.351
r_dihedral_angle_4_deg	15.506
r_dihedral_angle_3_deg	12.712
r_dihedral_angle_1_deg	6.311
r_angle_refined_deg	1.493
r_scangle_it	1.197
r_mcangle_it	0.9
r_scbond_it	0.725
r_mcbond_it	0.487
r_chiral_restr	0.108

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.351
r_dihedral_angle_4_deg	15.506
r_dihedral_angle_3_deg	12.712
r_dihedral_angle_1_deg	6.311
r_angle_refined_deg	1.493
r_scangle_it	1.197
r_mcangle_it	0.9
r_scbond_it	0.725
r_mcbond_it	0.487
r_chiral_restr	0.108
r_bond_refined_d	0.02
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8181
Nucleic Acid Atoms
Solvent Atoms	1284
Heterogen Atoms	766

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

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.