3LG1 | pdb_00003lg1

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase reduced by sodium borohydride (in complex with sulfite)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FO3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.7	278	Protein solution (2.5mcl): 9.3mg/ml TvNiR, 0.1M potassium phosphate (pH7.0). Reservoir solution (2.5mcl): 0.2M tri-sodium citrate dihydrate, 0.1M Tris hydrochloride (pH8.5), 30% v/v PEG 400. Crystals were soaked in 0.08M sodium sulfite, 0.13M sodium borohydride, 0.02M methyl viologen solution for 10min, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K

Crystal Properties
Matthews coefficient	Solvent content
4.18	70.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 192.62	α = 90
b = 192.62	β = 90
c = 192.62	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	MAR CCD 165 mm		2009-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	KURCHATOV SNC BEAMLINE K4.4	0.9886	KURCHATOV SNC	K4.4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.95	19.9	99.7	0.144	12.43		171816	171512			29.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	99.9		0.787	2.85		12457

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	3FO3	1.95	19.9	162890	8611	99.68	0.16178	0.16068	0.16	0.1826	0.19	RANDOM	20.984

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	37.499
r_dihedral_angle_4_deg	16.308
r_dihedral_angle_3_deg	12.965
r_dihedral_angle_1_deg	6.143
r_scangle_it	3.059
r_scbond_it	2.045
r_angle_refined_deg	1.54
r_mcangle_it	1.304
r_mcbond_it	0.735
r_chiral_restr	0.103

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.499
r_dihedral_angle_4_deg	16.308
r_dihedral_angle_3_deg	12.965
r_dihedral_angle_1_deg	6.143
r_scangle_it	3.059
r_scbond_it	2.045
r_angle_refined_deg	1.54
r_mcangle_it	1.304
r_mcbond_it	0.735
r_chiral_restr	0.103
r_bond_refined_d	0.018
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8212
Nucleic Acid Atoms
Solvent Atoms	974
Heterogen Atoms	912

Software

Software
Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

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.