3MMO

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.7278Protein solution (5mcl): 14.5mg/ml TvNiR, 0.05M Tris borate (pH8.7). Reservoir solution (5mcl): 0.2M tri-sodium citrate dihydrate, 0.1M Tris hydrochloride (pH8.5), 30% v/v PEG 400. Crystal was soaked in 0.1M KCN for 1h, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K
Crystal Properties
Matthews coefficientSolvent content
4.2370.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 194.56α = 90
b = 194.56β = 90
c = 194.56γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2004-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.81EMBL/DESY, HAMBURGX11

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
11.551299.90.04740.14.935056735025725.1
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)
11.551.571000.4213.94.811650

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 REPLACEMENTTHROUGHOUT2OT41.5511.983326211763699.660.148780.14810.16175RANDOM18.046
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_deg36.292
r_dihedral_angle_4_deg18.014
r_dihedral_angle_3_deg11.815
r_dihedral_angle_1_deg6.109
r_scangle_it3.228
r_scbond_it2.138
r_angle_refined_deg1.609
r_mcangle_it1.497
r_angle_other_deg0.977
r_mcbond_it0.904
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.292
r_dihedral_angle_4_deg18.014
r_dihedral_angle_3_deg11.815
r_dihedral_angle_1_deg6.109
r_scangle_it3.228
r_scbond_it2.138
r_angle_refined_deg1.609
r_mcangle_it1.497
r_angle_other_deg0.977
r_mcbond_it0.904
r_mcbond_other0.249
r_chiral_restr0.097
r_bond_refined_d0.02
r_gen_planes_refined0.016
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8217
Nucleic Acid Atoms
Solvent Atoms1218
Heterogen Atoms826

Software

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