6TFO

Crystal structure of as isolated three-domain copper-containing nitrite reductase from Hyphomicrobium denitrificans strain 1NES1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	20% (w/v) PEG 1,000, 0.1 M Sodium citrate tribasic dihydrate pH5.5, 0.1 M Lithium sulfate monohydrate

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.072	α = 90
b = 77.072	β = 90
c = 754.548	γ = 120

Symmetry
Space Group	P 65 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 EIGER X 16M		2019-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.05	66.75	98.7	0.121	0.084	0.995	3.5	4.3		85026			36.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.09	98.2		0.926	0.677	0.61	0.8	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	2DV6	2.05	66.58	80428	4195	98.29	0.2297	0.2271	0.2789	RANDOM	47.868

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]
2.1	1.05		2.1		-6.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.373
r_dihedral_angle_4_deg	23.051
r_dihedral_angle_3_deg	16.595
r_dihedral_angle_1_deg	8.63
r_angle_refined_deg	1.511
r_angle_other_deg	1.248
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.373
r_dihedral_angle_4_deg	23.051
r_dihedral_angle_3_deg	16.595
r_dihedral_angle_1_deg	8.63
r_angle_refined_deg	1.511
r_angle_other_deg	1.248
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9612
Nucleic Acid Atoms
Solvent Atoms	528
Heterogen Atoms	9

Software

Software
Software Name	Purpose
DIALS	data processing
Aimless	data scaling
MOLREP	phasing
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
DIALS	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.