9T6P | pdb_00009t6p

Higher-dose (283.1 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	33.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.542	α = 90
b = 96.542	β = 90
c = 96.542	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	2.016	29.117	100	0.402	0.417	0.124	0.991	5.8	11.2		20090			28.19

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	2.016	2.051	100		3.65	3.7	1.089	0.35	0.8	11.4	1013

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	2.008	29.109	20270	1004	99.847	0.159	0.1562	0.1658	0.2094	0.2038	30.316

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	14.686
r_dihedral_angle_3_deg	14.083
r_dihedral_angle_2_deg	9.411
r_dihedral_angle_1_deg	8.251
r_lrange_it	6.425
r_lrange_other	6.421
r_scangle_it	4.957
r_scangle_other	4.945
r_mcangle_it	3.513
r_mcangle_other	3.513
r_scbond_it	3.258
r_scbond_other	3.214
r_mcbond_it	2.372
r_mcbond_other	2.37
r_angle_refined_deg	1.697
r_angle_other_deg	0.812
r_symmetry_nbd_refined	0.206
r_nbd_other	0.206
r_symmetry_nbd_other	0.2
r_nbd_refined	0.197
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.15
r_symmetry_xyhbond_nbd_refined	0.142
r_metal_ion_refined	0.13
r_symmetry_nbtor_other	0.091
r_chiral_restr	0.075
r_symmetry_xyhbond_nbd_other	0.021
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2539
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	7

Software

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