8S5Y

MSOX movie series dataset 40 (22.8 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 = 104.26	α = 90
b = 104.26	β = 90
c = 64.66	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	1.3	64.66	100	0.163	0.184	0.084	0.998	11.5	9		98197

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	1.3	1.32			1.791	2.049	0.969	0.41		7.6

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	1.3	45.187	98169	5049	99.973	0.119	0.1177	0.1434	19.224

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		-0.059

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	17.514
r_dihedral_angle_6_deg	16.216
r_lrange_other	13.827
r_dihedral_angle_3_deg	11.389
r_dihedral_angle_2_deg	10.704
r_scangle_it	9.493
r_scangle_other	9.167
r_dihedral_angle_1_deg	7.508
r_scbond_it	6.609
r_mcangle_other	6.393
r_mcangle_it	6.378
r_scbond_other	6.321
r_mcbond_it	4.546
r_mcbond_other	4.529
r_rigid_bond_restr	3.678
r_angle_refined_deg	1.834
r_angle_other_deg	0.611
r_nbd_refined	0.235
r_xyhbond_nbd_refined	0.222
r_symmetry_xyhbond_nbd_refined	0.218
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.176
r_nbd_other	0.174
r_symmetry_nbd_refined	0.169
r_symmetry_xyhbond_nbd_other	0.165
r_metal_ion_refined	0.124
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.086
r_symmetry_metal_ion_refined	0.016
r_bond_refined_d	0.01
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	472
Heterogen Atoms	55

Software

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