9EVM

MSOX movie series dataset 30 (34.5 MGy) for nitrite bound 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	8RU9

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
2.55	51.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.56	α = 90
b = 104.56	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	0.77491	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	1.8	45.28	100	0.133	0.165	0.095	0.995	6.8	5.6		37438

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	1.8	1.84			1.23	1.518	0.873	0.365		5.7

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	1.8	30.002	37411	1873	99.925	0.153	0.1516	0.1833	28.482

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]
0.067	0.034		0.067		-0.218

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.546
r_dihedral_angle_3_deg	11.347
r_dihedral_angle_2_deg	8.798
r_dihedral_angle_1_deg	7.444
r_lrange_other	6.535
r_lrange_it	6.526
r_scangle_it	4.804
r_scangle_other	4.802
r_scbond_it	3.178
r_scbond_other	3.178
r_mcangle_it	2.992
r_mcangle_other	2.992
r_mcbond_it	2.11
r_mcbond_other	2.109
r_angle_refined_deg	1.707
r_angle_other_deg	0.553
r_nbd_refined	0.22
r_xyhbond_nbd_refined	0.196
r_symmetry_nbd_other	0.189
r_symmetry_xyhbond_nbd_refined	0.178
r_nbtor_refined	0.175
r_nbd_other	0.148
r_symmetry_xyhbond_nbd_other	0.131
r_metal_ion_refined	0.121
r_symmetry_nbd_refined	0.117
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.082
r_xyhbond_nbd_other	0.024
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2558
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms	51

Software

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