8S2Q

MSOX movie series dataset 2 (1.14 MGy) for as isolated BrJNiR (Cu containing nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110) at pH 8.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8S0W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	100 mM Tris pH 7.3, 1.8 M Ammonium Sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.82	α = 90
b = 103.82	β = 90
c = 64.35	γ = 120

Symmetry
Space Group	P 63

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		2023-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.775	Diamond	I24

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	1.05	64.35	100	0.082	0.093	0.042	0.999	11.8	8.1		183378

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	1.05	1.07			1.732	2.022	0.995	0.386		6.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.05	52.383	183344	9116	99.995	0.115	0.1147	0.1295	16.116

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]
0.018	0.009		0.018		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	19.325
r_dihedral_angle_6_deg	16.24
r_lrange_other	14.529
r_dihedral_angle_2_deg	12.07
r_dihedral_angle_3_deg	11.65
r_scangle_it	8.956
r_scangle_other	8.658
r_mcangle_other	7.879
r_dihedral_angle_1_deg	7.861
r_mcangle_it	7.766
r_scbond_it	6.321
r_scbond_other	5.936
r_mcbond_it	5.746
r_mcbond_other	5.464
r_rigid_bond_restr	4.069
r_angle_refined_deg	2.002
r_angle_other_deg	0.693
r_nbd_refined	0.251
r_xyhbond_nbd_refined	0.23
r_symmetry_xyhbond_nbd_refined	0.201
r_symmetry_nbd_other	0.193
r_nbd_other	0.183
r_nbtor_refined	0.179
r_symmetry_nbd_refined	0.127
r_chiral_restr	0.105
r_metal_ion_refined	0.093
r_symmetry_nbtor_other	0.088
r_symmetry_xyhbond_nbd_other	0.028
r_symmetry_metal_ion_refined	0.028
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2551
Nucleic Acid Atoms
Solvent Atoms	529
Heterogen Atoms	55

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
REFMAC	phasing