3F29 | pdb_00003f29

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

X-RAY DIFFRACTION

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% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K

Crystal Properties
Matthews coefficient	Solvent content
4.23	70.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 193.568	α = 90
b = 193.568	β = 90
c = 193.568	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		2005-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B	0.840	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	2	30	97.6	0.06	25.5		192707	157823

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	2.02	2.08	97.7		0.062	13.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2	19.97	149777	8007	97.48	0.15476	0.15375	0.16	0.17395	RANDOM	21.599

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	36.71
r_dihedral_angle_4_deg	16.503
r_dihedral_angle_3_deg	12.661
r_dihedral_angle_1_deg	5.875
r_scangle_it	2.316
r_scbond_it	1.573
r_angle_refined_deg	1.259
r_mcangle_it	1.008
r_mcbond_it	0.62
r_nbtor_refined	0.294

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.71
r_dihedral_angle_4_deg	16.503
r_dihedral_angle_3_deg	12.661
r_dihedral_angle_1_deg	5.875
r_scangle_it	2.316
r_scbond_it	1.573
r_angle_refined_deg	1.259
r_mcangle_it	1.008
r_mcbond_it	0.62
r_nbtor_refined	0.294
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.166
r_xyhbond_nbd_refined	0.115
r_symmetry_hbond_refined	0.084
r_chiral_restr	0.082
r_metal_ion_refined	0.048
r_bond_refined_d	0.012
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8204
Nucleic Acid Atoms
Solvent Atoms	1086
Heterogen Atoms	795

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.