9KVL | pdb_00009kvl

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

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
3.03	59.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.06	α = 90
b = 115.06	β = 90
c = 84.483	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	100	DIFFRACTOMETER	iBIX		2020-01-28	L	LAUE
2	1	x-ray	100	PIXEL	DECTRIS PILATUS3 S 2M		2020-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SPALLATION SOURCE	J-PARC MLF BEAMLINE BL-03	2.15-4.89	JPARC MLF	BL-03
2	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	0.8	Photon Factory	AR-NW12A

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	1.7	20	94.6	0.247			0.096	0.973		8.8	7.3		43445			6.43
2	1	42.92	100	0.076			0.037	0.996		13.3	5.1		225316			6.43

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	1.7	1.79		0.565			0.243	0.778		3	5.8
2	1	1.02		0.33			0.162	0.94		4.6	5.1

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
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	1.7	13.2				43442	2003	94.84		0.1564	0.1556		0.1718
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.3	28.16				102513		99.92			0.1144	0.1145	0.1316	0.1315

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	16.335
f_angle_d	1.134
f_chiral_restr	0.088
f_bond_d	0.02
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2328
Nucleic Acid Atoms
Solvent Atoms	336
Heterogen Atoms	22

Software

Software
Software Name	Purpose
PHENIX	refinement
STARGazer	data reduction
autoXDS	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.