8RUR

High pH (8.0) nitrite-bound MSOX movie series dataset 2 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [1.38 MGy]

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	7	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		2023-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.7749	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	1.13	45.039	99.6	0.078	0.087	0.038	0.998	8.7	4.4		146809

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.13	1.15	99.2		0.916	0.575	0.449	1.3	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	1.13	45.004	146783	7537	99.629	0.117	0.1156	0.1339	15.997

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]
-0.203	-0.101		-0.203		0.658

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_other	20.116
r_lrange_it	20.115
r_dihedral_angle_6_deg	16.401
r_dihedral_angle_3_deg	12.249
r_dihedral_angle_2_deg	11.989
r_scangle_it	9.418
r_scangle_other	9.416
r_dihedral_angle_1_deg	7.955
r_scbond_it	7.308
r_scbond_other	7.306
r_mcangle_other	7.135
r_mcangle_it	7.132
r_mcbond_it	5.104
r_mcbond_other	5.098
r_rigid_bond_restr	4.732
r_angle_refined_deg	2.002
r_angle_other_deg	0.716
r_symmetry_xyhbond_nbd_refined	0.289
r_nbd_refined	0.25
r_symmetry_nbd_refined	0.219
r_xyhbond_nbd_refined	0.208
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.179
r_nbd_other	0.171
r_chiral_restr	0.109
r_symmetry_nbtor_other	0.088
r_symmetry_xyhbond_nbd_other	0.062
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_xyhbond_nbd_other	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2558
Nucleic Acid Atoms
Solvent Atoms	502
Heterogen Atoms	53

Software

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