3LG1

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FO3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.7278Protein solution (2.5mcl): 9.3mg/ml TvNiR, 0.1M potassium phosphate (pH7.0). Reservoir solution (2.5mcl): 0.2M tri-sodium citrate dihydrate, 0.1M Tris hydrochloride (pH8.5), 30% v/v PEG 400. Crystals were soaked in 0.08M sodium sulfite, 0.13M sodium borohydride, 0.02M methyl viologen solution for 10min, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K
Crystal Properties
Matthews coefficientSolvent content
4.1870.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 192.62α = 90
b = 192.62β = 90
c = 192.62γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2009-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONKURCHATOV SNC BEAMLINE K4.40.9886KURCHATOV SNCK4.4

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
11.9519.999.70.14412.4317181617151229.2
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)
11.95299.90.7872.8512457

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3FO31.9519.9162890861199.680.161780.160680.1826RANDOM20.984
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_deg37.499
r_dihedral_angle_4_deg16.308
r_dihedral_angle_3_deg12.965
r_dihedral_angle_1_deg6.143
r_scangle_it3.059
r_scbond_it2.045
r_angle_refined_deg1.54
r_mcangle_it1.304
r_mcbond_it0.735
r_chiral_restr0.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.499
r_dihedral_angle_4_deg16.308
r_dihedral_angle_3_deg12.965
r_dihedral_angle_1_deg6.143
r_scangle_it3.059
r_scbond_it2.045
r_angle_refined_deg1.54
r_mcangle_it1.304
r_mcbond_it0.735
r_chiral_restr0.103
r_bond_refined_d0.018
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8212
Nucleic Acid Atoms
Solvent Atoms974
Heterogen Atoms912

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling