8S64

MSOX movie series dataset 10 (9.5 MGy) for as isolated BrJNiR (Cu containing nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110) at pH 5.5.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8R8S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	50 mM Hepes pH 5.5, 1.8 M Ammonium Sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.22	α = 90
b = 104.22	β = 90
c = 64.72	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		2022-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.855	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	1.42	52.164	99.5	0.063	0.078	0.045	0.998	10.8	4.6		75045

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	1.42	1.44			1.487	1.819	1.018	0.338		3.8

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	1.42	52.164	75019	3794	99.376	0.147	0.1456	0.171	21.609

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]
-0.281	-0.141		-0.281		0.913

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.791
r_dihedral_angle_3_deg	11.483
r_dihedral_angle_2_deg	10.275
r_dihedral_angle_1_deg	7.518
r_lrange_it	6.093
r_lrange_other	6.093
r_scangle_it	4.309
r_scangle_other	4.308
r_scbond_it	2.822
r_scbond_other	2.822
r_mcangle_it	2.72
r_mcangle_other	2.692
r_mcbond_it	1.966
r_mcbond_other	1.966
r_angle_refined_deg	1.905
r_angle_other_deg	0.642
r_symmetry_xyhbond_nbd_refined	0.305
r_xyhbond_nbd_refined	0.223
r_symmetry_nbd_refined	0.219
r_nbd_refined	0.208
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.178
r_nbd_other	0.171
r_symmetry_xyhbond_nbd_other	0.133
r_metal_ion_refined	0.111
r_chiral_restr	0.098
r_symmetry_nbtor_other	0.087
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	2561
Nucleic Acid Atoms
Solvent Atoms	436
Heterogen Atoms	45

Software

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