6ZAU | pdb_00006zau

Damage-free nitrite-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) determined by serial femtosecond rotation crystallography

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	291	1.6/1.8 M (NH4)2SO4 and 50mM HEPES buffer pH 5/ pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.6	56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.95	α = 90
b = 106.95	β = 90
c = 106.95	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	CCD	RAYONIX MX300-HS		2020-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL2	1.2398	SACLA	BL2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (All)	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	1.3	75.63	99.9	0.951	0.163	4.1	73.4		99872			16.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.35	99.5		0.016	1.126	1.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6THF	1.3	29.8	99687	5033	99.9	0.1583	0.1558	0.16	0.2061	0.21	RANDOM	22.613

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_2_deg	35.631
r_dihedral_angle_4_deg	20.814
r_dihedral_angle_3_deg	13.402
r_dihedral_angle_1_deg	8.361
r_rigid_bond_restr	3.333
r_angle_refined_deg	1.903
r_angle_other_deg	1.514
r_chiral_restr	0.104
r_bond_refined_d	0.015
r_gen_planes_refined	0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.631
r_dihedral_angle_4_deg	20.814
r_dihedral_angle_3_deg	13.402
r_dihedral_angle_1_deg	8.361
r_rigid_bond_restr	3.333
r_angle_refined_deg	1.903
r_angle_other_deg	1.514
r_chiral_restr	0.104
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2662
Nucleic Acid Atoms
Solvent Atoms	459
Heterogen Atoms	103

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.