9T6O | pdb_00009t6o

Low-dose (14.9 kGy) structure of copper-containing nitrite reductase from Achromobacter cycloclastes at room temperature

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ZU6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.75	293	Crystals were grown using the vapor diffusion hanging drop method with a protein concentration of 10 mg/ml. The reservoir solution consisted of 1.6 M ammonium sulfate and 0.1 M sodium acetate (pH 4.75).

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.472	α = 90
b = 96.472	β = 90
c = 96.472	γ = 90

Symmetry
Space Group	P 21 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	DECTRIS PILATUS 6M		2025-05-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM07	0.9795	ESRF	BM07

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	1.605	26.756	100	0.04085	0.248	0.074	0.995	7	11.2		39308			19.42

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	1.605	1.633	100		3.652	3.896	1.148	0.333	0.6	11.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.597	27.865	39824	1986	99.797	0.151	0.1493	0.1622	0.179	0.1844	21.026

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.07
r_dihedral_angle_3_deg	13.321
r_dihedral_angle_2_deg	8.465
r_dihedral_angle_1_deg	7.874
r_lrange_it	5.312
r_lrange_other	5.249
r_scangle_it	4.208
r_scangle_other	4.208
r_scbond_it	2.719
r_scbond_other	2.714
r_mcangle_it	2.628
r_mcangle_other	2.627
r_mcbond_it	1.757
r_mcbond_other	1.754
r_angle_refined_deg	1.629
r_angle_other_deg	0.562
r_symmetry_nbd_refined	0.288
r_nbd_other	0.222
r_nbd_refined	0.204
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.157
r_metal_ion_refined	0.141
r_symmetry_xyhbond_nbd_refined	0.14
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.082
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	2543
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	7

Software

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