3RKH

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with nitrite (full occupancy)

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		278	Protein solution (2.5 uL): 11.6 mg/mL TvNiR, 0.05 M Tris-HCl, pH 8.0, reservoir solution (2.5 uL): 0.2 M ammonium acetate, 0.1 M citric acid trisodium salt, pH 5.6, 30% MPD, 0.1 M sodium nitrite, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K

Crystal Properties
Matthews coefficient	Solvent content
5.066891	75.724762

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 192.8	α = 90
b = 192.8	β = 90
c = 192.8	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		2010-06-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	KURCHATOV SNC BEAMLINE K4.4		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	1.83	136.33	99.8	0.12	20			208153			26.2

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	1.83	1.9	99.9		0.671	3.9

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	1.83	100	197647	10466	99.85	0.14239	0.14137	0.16196	RANDOM	21.013

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	36.999
r_dihedral_angle_4_deg	18.945
r_dihedral_angle_3_deg	12.468
r_dihedral_angle_1_deg	6.294
r_scangle_it	3.544
r_scbond_it	2.325
r_angle_refined_deg	1.7
r_mcangle_it	1.498
r_mcbond_it	0.874
r_chiral_restr	0.11
r_bond_refined_d	0.02
r_gen_planes_refined	0.016
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	8239
Nucleic Acid Atoms
Solvent Atoms	1327
Heterogen Atoms	712

Software

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