3LGQ

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with sulfite (modified Tyr-303)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GM6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5278Protein solution (2.5mcl): 10mg/ml TvNiR, 0.05M Tris hydrochloride (pH7.2). Reservoir solution (2.5mcl): 0.2M ammonium acetate, 0.1M tri-sodium citrate dihydrate, 30% v/v 2-methyl-2,4-pentanediol, 0.1M sodium sulfite (pH6.5), VAPOR DIFFUSION, HANGING DROP, temperature 278.0K
Crystal Properties
Matthews coefficientSolvent content
4.3671.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 195.69α = 90
b = 195.69β = 90
c = 195.69γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2009-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8123EMBL/DESY, HAMBURGX13

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
11.819.896.60.06615.1322894622117028
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)
11.81.8573.10.393.117909

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 REPLACEMENTTHROUGHOUT3GM61.819.82100801109097.620.151340.150480.1675RANDOM25.163
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_deg36.669
r_dihedral_angle_4_deg17.734
r_dihedral_angle_3_deg13.065
r_dihedral_angle_1_deg6.09
r_scangle_it3.112
r_scbond_it2.006
r_angle_refined_deg1.47
r_mcangle_it1.26
r_mcbond_it0.688
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.669
r_dihedral_angle_4_deg17.734
r_dihedral_angle_3_deg13.065
r_dihedral_angle_1_deg6.09
r_scangle_it3.112
r_scbond_it2.006
r_angle_refined_deg1.47
r_mcangle_it1.26
r_mcbond_it0.688
r_chiral_restr0.107
r_bond_refined_d0.018
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8232
Nucleic Acid Atoms
Solvent Atoms1140
Heterogen Atoms742

Software

Software
Software NamePurpose
DNAdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling