6ZAW

Damage-free NO-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) determined by serial femtosecond rotation crystallography

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		297	1.6/1.8 M (NH4)2SO2 and 50mM HEPES buffer pH 5/ pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.87	α = 90
b = 106.87	β = 90
c = 106.87	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	RAYONIX MX300-HS		2020-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL2	1.240	SACLA	BL2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	R Split (All)	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	1.25	31	100	0.055	0.967	0.034	6.5	138.8		106311			13.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.25	1.3	100		0.503	0.491	0.491	2.3	64.1

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	6THF	1.3	30.87	94625	5014	99.99	0.1372	0.135	0.1798	RANDOM	19.054

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	34.657
r_dihedral_angle_4_deg	22.136
r_dihedral_angle_3_deg	12.514
r_dihedral_angle_1_deg	7.945
r_rigid_bond_restr	3.757
r_angle_refined_deg	2.064
r_angle_other_deg	1.568
r_chiral_restr	0.111
r_bond_refined_d	0.017
r_gen_planes_refined	0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.657
r_dihedral_angle_4_deg	22.136
r_dihedral_angle_3_deg	12.514
r_dihedral_angle_1_deg	7.945
r_rigid_bond_restr	3.757
r_angle_refined_deg	2.064
r_angle_other_deg	1.568
r_chiral_restr	0.111
r_bond_refined_d	0.017
r_gen_planes_refined	0.013
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2662
Nucleic Acid Atoms
Solvent Atoms	516
Heterogen Atoms	156

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
Aimless	data scaling
REFMAC	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.