3FO3

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OT4	PDB ENTRY 2OT4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.7	278	Protein solution (5mcl): 14.5mg/ml TvNiR, 0.005M Tris borate (pH8.7). Reservoir solution (5mcl): 0.2M tri-sodium citrate dihydrate, 0.1M Tris hydrochloride (pH8.5), 30% v/v PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K

Crystal Properties
Matthews coefficient	Solvent content
4.06	69.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 193.79	α = 90
b = 193.79	β = 90
c = 193.79	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	IMAGE PLATE	MAR scanner 345 mm plate		2004-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B	0.843	EMBL/DESY, HAMBURG	BW7B

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	1.4	12	99.7	0.055	33.1		469642	468027

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	1.4	1.42	100		0.547	2.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2OT4	1.4	12	443992	23479	99.38	0.12663	0.12595	0.13946	RANDOM	17.514

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	36.27
r_dihedral_angle_4_deg	16.213
r_dihedral_angle_3_deg	12.076
r_sphericity_free	7.641
r_dihedral_angle_1_deg	5.954
r_sphericity_bonded	3.834
r_scangle_it	3.358
r_scbond_it	2.445
r_mcangle_it	1.821
r_angle_refined_deg	1.558
r_rigid_bond_restr	1.385
r_mcbond_it	1.232
r_angle_other_deg	0.973
r_mcbond_other	0.708
r_symmetry_vdw_other	0.327
r_nbd_refined	0.22
r_nbd_other	0.214
r_nbtor_refined	0.207
r_symmetry_vdw_refined	0.18
r_symmetry_metal_ion_refined	0.15
r_symmetry_hbond_refined	0.123
r_metal_ion_refined	0.116
r_nbtor_other	0.112
r_xyhbond_nbd_refined	0.112
r_chiral_restr	0.095
r_bond_refined_d	0.018
r_gen_planes_refined	0.016
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8217
Nucleic Acid Atoms
Solvent Atoms	1385
Heterogen Atoms	922

Software

Software
Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling