8S69

MSOX movie series dataset 40 (38 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 = 104.29	α = 90
b = 104.29	β = 90
c = 64.79	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		2022-07-18	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	1.78	52.65	99.6	0.137	0.17	0.099	0.994	8.5	4.9		38372

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	1.78	1.82			1.316	1.637	0.948	0.314		5

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	1.78	52.199	38353	1926	99.448	0.158	0.1562	0.1928	28.284

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]
-0.289	-0.144		-0.289		0.937

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.234
r_dihedral_angle_3_deg	11.96
r_dihedral_angle_2_deg	9.546
r_dihedral_angle_1_deg	7.419
r_lrange_it	6.895
r_lrange_other	6.663
r_scangle_it	5.143
r_scangle_other	5.089
r_scbond_it	3.338
r_scbond_other	3.24
r_mcangle_it	3.085
r_mcangle_other	3.085
r_mcbond_it	2.117
r_mcbond_other	2.117
r_angle_refined_deg	1.666
r_angle_other_deg	0.575
r_symmetry_xyhbond_nbd_refined	0.236
r_nbd_refined	0.195
r_xyhbond_nbd_refined	0.19
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.181
r_symmetry_xyhbond_nbd_other	0.157
r_nbd_other	0.143
r_symmetry_nbd_refined	0.114
r_symmetry_nbtor_other	0.087
r_metal_ion_refined	0.086
r_chiral_restr	0.083
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	2554
Nucleic Acid Atoms
Solvent Atoms	295
Heterogen Atoms	45

Software

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