3SCE

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase with a covalent bond between the CE1 atom of Tyr303 and the CG atom of Gln360 (TvNiRb)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.7	278	Protein solution (2.5 uL): 9.3 mg/mL TvNiRb, 0.1 M potassium phosphate, pH 7.0, Reservoir solution (2.5 uL): 0.2 M tri-sodium citrate dihydrate, 0.1 M Tris hydrochloride, pH8.5, 30% v/v PEG400 , VAPOR DIFFUSION, HANGING DROP, temperature 278.0 K

Crystal Properties
Matthews coefficient	Solvent content
5.09	75.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 193	α = 90
b = 193	β = 90
c = 193	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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU		SPring-8	BL41XU

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	1.45	136.472	99.9	0.11	11.1			464187			21.2

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	1.45	1.6	99.9		0.544	3.4

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	1.45	100	397225	20931	99.91	0.12468	0.12385	0.14041	RANDOM	14.342

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	36.488
r_dihedral_angle_4_deg	16.519
r_dihedral_angle_3_deg	11.959
r_sphericity_free	7.429
r_dihedral_angle_1_deg	6.122
r_scangle_it	4.415
r_sphericity_bonded	4.147
r_scbond_it	2.963
r_mcangle_it	1.981
r_rigid_bond_restr	1.794
r_angle_refined_deg	1.46
r_mcbond_it	1.216
r_angle_other_deg	1.098
r_mcbond_other	0.648
r_chiral_restr	0.089
r_bond_refined_d	0.017
r_gen_planes_refined	0.015
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8231
Nucleic Acid Atoms
Solvent Atoms	1186
Heterogen Atoms	867

Software

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