9KVM | pdb_00009kvm

Neutron and X-ray joint refined structure of a copper-containing nitrite reductase (C135A mutant) in complex with formate

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4YSO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	0.1 M acetate buffer pH 4.5, 5.5% (w/v) PEG 4000, and 75 mM CuSO4

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.172	α = 90
b = 116.172	β = 90
c = 85.612	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	neutron	298	DIFFRACTOMETER	iBIX		2021-05-13	L	LAUE
2	1	x-ray	298	PIXEL	DECTRIS PILATUS3 S 6M		2021-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SPALLATION SOURCE	J-PARC MLF BEAMLINE BL-03	2.44-5.28	JPARC MLF	BL-03
2	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

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)	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	1.9	20	97.7	0.264			0.108	0.975		6.5	6.8		33212			12.78
2	1.2	43.4	100	0.088			0.021	0.996		9.7	5.1		134752			12.78

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2		0.89			0.428	0.527		1.7	5.1
2	1.2	1.22		0.9			0.253	0.701		1.7	5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.2	39.39		1.97		134742	3999	99.98		0.1141	0.1139	0.113	0.1185	0.1184		30
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	1.9	12.9				33208		96.94			0.146		0.183

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
f_dihedral_angle_d	16.5797
f_angle_d	1.1745
f_chiral_restr	0.0908
f_bond_d	0.0217
f_plane_restr	0.0065

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2335
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms	7

Software

Software
Software Name	Purpose
PHENIX	refinement
STARGazer	data reduction
XDS	data reduction
SCALA	data scaling
MOLREP	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.