3D1I

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with nitrite

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	8.5	278	The drop contained 5ml of enzyme solution (14.5mg/ml) in 0.005M Tris-borat buffer (PH8.7) and 5ml reservoir solution. The reservoir solution contained 27% PEG400, 0.18M sodium citrate in 0.09M Tris buffer (PH8.5), complex with nitrite ion was obtained by soaking crystal in reservoir solution with 100mM sodium nitrite by 30 minute, VAPOR DIFFUSION, HANGING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
5.07	75.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 193.412	α = 90
b = 193.412	β = 90
c = 193.412	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	EMBL/DESY, HAMBURG BEAMLINE X13		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	13	99.7	0.079	16			228600

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	1.82	98.8		0.6

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	1.8	11.99	208802	11051	99.47	0.14936	0.1485	0.16547	RANDOM	16.63

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	36.367
r_dihedral_angle_4_deg	18.029
r_dihedral_angle_3_deg	12.419
r_dihedral_angle_1_deg	6.127
r_scangle_it	3.368
r_scbond_it	2.238
r_angle_refined_deg	1.641
r_mcangle_it	1.408
r_angle_other_deg	1.049
r_mcbond_it	0.841
r_symmetry_vdw_other	0.301
r_mcbond_other	0.271
r_nbd_refined	0.223
r_nbd_other	0.215
r_nbtor_refined	0.19
r_xyhbond_nbd_refined	0.141
r_symmetry_hbond_refined	0.139
r_symmetry_vdw_refined	0.118
r_chiral_restr	0.114
r_symmetry_metal_ion_refined	0.095
r_nbtor_other	0.094
r_metal_ion_refined	0.078
r_bond_refined_d	0.021
r_gen_planes_refined	0.014
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8225
Nucleic Acid Atoms
Solvent Atoms	1130
Heterogen Atoms	767

Software

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