9T6Q | pdb_00009t6q

Low-dose (33.3 kGy) structure of copper-containing nitrite reductase from Achromobacter cycloclastes at cryogenic temperature

X-RAY DIFFRACTION

---

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	38.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.352	α = 90
b = 95.352	β = 90
c = 95.352	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	100	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)	R Sym 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	1.464	27.53	99.9	0.219	0.23	0.21	0.062	0.997	9.1	11.2		49834

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	1.464	1.489	98.1		2.611	2.306	0.729	0.354	1	9.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.465	28.75	49728	2493	99.857	0.157	0.1552	0.1556	0.191	0.1911	14.009

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	15.029
r_dihedral_angle_3_deg	12.382
r_dihedral_angle_1_deg	8.18
r_dihedral_angle_2_deg	7.168
r_lrange_it	4.325
r_lrange_other	4.071
r_scangle_it	2.626
r_scangle_other	2.501
r_mcangle_it	1.847
r_mcangle_other	1.847
r_scbond_it	1.681
r_angle_refined_deg	1.669
r_scbond_other	1.578
r_mcbond_it	1.177
r_mcbond_other	1.177
r_angle_other_deg	0.582
r_nbd_refined	0.212
r_nbd_other	0.209
r_symmetry_xyhbond_nbd_refined	0.195
r_symmetry_nbd_other	0.194
r_symmetry_nbd_refined	0.191
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.155
r_metal_ion_refined	0.117
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.087
r_symmetry_xyhbond_nbd_other	0.012
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	2561
Nucleic Acid Atoms
Solvent Atoms	391
Heterogen Atoms	60

Software

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