3S7W

Structure of the TvNiRb form of Thioalkalivibrio nitratireducens cytochrome c nitrite reductase with an oxidized Gln360 in a complex with hydroxylamine

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	7.5	278	Protein solution (2.5mcl): 10.0 mg/ml TvNiRb, 0.05M Tris-HCl (pH7.2). Reservoir solution (2.5mcl): 1.26M tri-sodium citrate dihydrate, 0.09M HEPES/NaOH, 10% v/v glycerol, 0.1M hydroxylamine., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K

Crystal Properties
Matthews coefficient	Solvent content
5.24	71.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 194.89	α = 90
b = 194.89	β = 90
c = 194.89	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	0.812	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	1.79	19.7	97.2	0.071	12.6			223578

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	1.79	1.85	84.7		0.449	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	1.79	19.7	212354	11224	97.6	0.15408	0.1531	0.17247	RANDOM	27.743

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	36.579
r_dihedral_angle_4_deg	16.672
r_dihedral_angle_3_deg	12.686
r_dihedral_angle_1_deg	6.115
r_scangle_it	3.178
r_scbond_it	2.086
r_angle_refined_deg	1.459
r_mcangle_it	1.271
r_mcbond_it	0.718
r_chiral_restr	0.104
r_bond_refined_d	0.019
r_gen_planes_refined	0.014
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8229
Nucleic Acid Atoms
Solvent Atoms	1088
Heterogen Atoms	744

Software

Software
Software Name	Purpose
DNA	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling