3LGQ | pdb_00003lgq

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with sulfite (modified Tyr-303)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GM6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	278	Protein solution (2.5mcl): 10mg/ml TvNiR, 0.05M Tris hydrochloride (pH7.2). Reservoir solution (2.5mcl): 0.2M ammonium acetate, 0.1M tri-sodium citrate dihydrate, 30% v/v 2-methyl-2,4-pentanediol, 0.1M sodium sulfite (pH6.5), VAPOR DIFFUSION, HANGING DROP, temperature 278.0K

Crystal Properties
Matthews coefficient	Solvent content
4.36	71.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 195.69	α = 90
b = 195.69	β = 90
c = 195.69	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		2009-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8123	EMBL/DESY, HAMBURG	X13

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	1.8	19.8	96.6	0.066	15.1	3	228946	221170			28

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	1.8	1.85	73.1		0.39	3.1		17909

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	3GM6	1.8	19.8	210080	11090	97.62	0.15134	0.15048	0.16	0.1675	0.17	RANDOM	25.163

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	36.669
r_dihedral_angle_4_deg	17.734
r_dihedral_angle_3_deg	13.065
r_dihedral_angle_1_deg	6.09
r_scangle_it	3.112
r_scbond_it	2.006
r_angle_refined_deg	1.47
r_mcangle_it	1.26
r_mcbond_it	0.688
r_chiral_restr	0.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.669
r_dihedral_angle_4_deg	17.734
r_dihedral_angle_3_deg	13.065
r_dihedral_angle_1_deg	6.09
r_scangle_it	3.112
r_scbond_it	2.006
r_angle_refined_deg	1.47
r_mcangle_it	1.26
r_mcbond_it	0.688
r_chiral_restr	0.107
r_bond_refined_d	0.018
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8232
Nucleic Acid Atoms
Solvent Atoms	1140
Heterogen Atoms	742

Software

Software
Software Name	Purpose
DNA	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.