3D1I

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5278The drop contained 5ml of enzyme solution (14.5mg/ml) in 0.005M Tris-borat buffer (PH8.7) and 5ml reservoir solution. The reservoir solution contained 27% PEG400, 0.18M sodium citrate in 0.09M Tris buffer (PH8.5), complex with nitrite ion was obtained by soaking crystal in reservoir solution with 100mM sodium nitrite by 30 minute, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
5.0775.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 193.412α = 90
b = 193.412β = 90
c = 193.412γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/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
11.81399.70.07916228600
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)
11.81.8298.80.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2OT41.811.992088021105199.470.149360.14850.16547RANDOM16.63
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_deg36.367
r_dihedral_angle_4_deg18.029
r_dihedral_angle_3_deg12.419
r_dihedral_angle_1_deg6.127
r_scangle_it3.368
r_scbond_it2.238
r_angle_refined_deg1.641
r_mcangle_it1.408
r_angle_other_deg1.049
r_mcbond_it0.841
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.367
r_dihedral_angle_4_deg18.029
r_dihedral_angle_3_deg12.419
r_dihedral_angle_1_deg6.127
r_scangle_it3.368
r_scbond_it2.238
r_angle_refined_deg1.641
r_mcangle_it1.408
r_angle_other_deg1.049
r_mcbond_it0.841
r_symmetry_vdw_other0.301
r_mcbond_other0.271
r_nbd_refined0.223
r_nbd_other0.215
r_nbtor_refined0.19
r_xyhbond_nbd_refined0.141
r_symmetry_hbond_refined0.139
r_symmetry_vdw_refined0.118
r_chiral_restr0.114
r_symmetry_metal_ion_refined0.095
r_nbtor_other0.094
r_metal_ion_refined0.078
r_bond_refined_d0.021
r_gen_planes_refined0.014
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8225
Nucleic Acid Atoms
Solvent Atoms1130
Heterogen Atoms767

Software

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