3FO3 | pdb_00003fo3

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase reduced by sodium dithionite (sulfite complex)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OT4PDB ENTRY 2OT4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.7278Protein 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% v/v PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K
Crystal Properties
Matthews coefficientSolvent content
4.0669.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 193.79α = 90
b = 193.79β = 90
c = 193.79γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2004-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7B0.843EMBL/DESY, HAMBURGBW7B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.41299.70.05533.1469642468027
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.421000.5472.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2OT41.4124439922347999.380.126630.125950.140.139460.15RANDOM17.514
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.27
r_dihedral_angle_4_deg16.213
r_dihedral_angle_3_deg12.076
r_sphericity_free7.641
r_dihedral_angle_1_deg5.954
r_sphericity_bonded3.834
r_scangle_it3.358
r_scbond_it2.445
r_mcangle_it1.821
r_angle_refined_deg1.558
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.27
r_dihedral_angle_4_deg16.213
r_dihedral_angle_3_deg12.076
r_sphericity_free7.641
r_dihedral_angle_1_deg5.954
r_sphericity_bonded3.834
r_scangle_it3.358
r_scbond_it2.445
r_mcangle_it1.821
r_angle_refined_deg1.558
r_rigid_bond_restr1.385
r_mcbond_it1.232
r_angle_other_deg0.973
r_mcbond_other0.708
r_symmetry_vdw_other0.327
r_nbd_refined0.22
r_nbd_other0.214
r_nbtor_refined0.207
r_symmetry_vdw_refined0.18
r_symmetry_metal_ion_refined0.15
r_symmetry_hbond_refined0.123
r_metal_ion_refined0.116
r_nbtor_other0.112
r_xyhbond_nbd_refined0.112
r_chiral_restr0.095
r_bond_refined_d0.018
r_gen_planes_refined0.016
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8217
Nucleic Acid Atoms
Solvent Atoms1385
Heterogen Atoms922

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling