8RFP

Low pH (5.5) nitrite-bound MSOX movie series dataset 3 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [3.06 MGy] - nitrite/NO intermediate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	293	0.1 M Tris pH 7.3, 1.8 M Ammonium Sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.21	α = 90
b = 104.21	β = 90
c = 64.37	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		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)	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	1.23	45.12	99.1	0.031	0.999	10.7	5.1		114182			13.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.23	1.25	98.4		0.84	0.333	0.9	4.3

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.23	30	108320	5838	99.08	0.11549	0.11431	0.13767	RANDOM	17.696

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]
-0.22	-0.11		-0.22		0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	13.575
r_dihedral_angle_3_deg	12.724
r_long_range_B_other	11.979
r_dihedral_angle_2_deg	11.333
r_scangle_other	9.101
r_dihedral_angle_1_deg	7.815
r_scbond_it	6.797
r_mcangle_other	6.476
r_mcangle_it	6.472
r_scbond_other	6.422
r_mcbond_it	4.705
r_mcbond_other	4.665
r_rigid_bond_restr	3.842
r_angle_refined_deg	1.862
r_angle_other_deg	0.665
r_chiral_restr	0.1
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2562
Nucleic Acid Atoms
Solvent Atoms	397
Heterogen Atoms	66

Software

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