8RU9

MSOX movie series dataset 1 (1.12 MGy) for nitrite bound BrJNiR (Cu containing nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 at pH 8.

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	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 = 103.92	α = 90
b = 103.92	β = 90
c = 64.25	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 PILATUS3 6M		2023-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.77492	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	1.1	45.039	99.6	0.068	0.085	0.05	0.998	8.1	4.3		159037

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	1.1	1.12	99.27		1.115	1	0.858	0.313		3.2

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	1.1	45.039	159007	8211	99.616	0.121	0.1197	0.1374	15.696

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]
-0.108	-0.054		-0.108		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.128
r_lrange_it	15.792
r_lrange_other	12
r_dihedral_angle_3_deg	11.641
r_dihedral_angle_2_deg	11.024
r_scangle_it	8.007
r_dihedral_angle_1_deg	7.929
r_scangle_other	7.594
r_mcangle_other	6.67
r_mcangle_it	6.664
r_scbond_it	5.928
r_scbond_other	5.46
r_mcbond_it	4.705
r_mcbond_other	4.69
r_rigid_bond_restr	3.979
r_angle_refined_deg	1.863
r_angle_other_deg	0.648
r_symmetry_xyhbond_nbd_other	0.414
r_nbd_refined	0.275
r_symmetry_xyhbond_nbd_refined	0.252
r_xyhbond_nbd_refined	0.199
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.179
r_symmetry_nbd_refined	0.179
r_nbd_other	0.155
r_metal_ion_refined	0.12
r_chiral_restr	0.1
r_symmetry_nbtor_other	0.086
r_symmetry_metal_ion_refined	0.022
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	2559
Nucleic Acid Atoms
Solvent Atoms	530
Heterogen Atoms	53

Software

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