2OT4 | pdb_00002ot4

Structure of a hexameric multiheme c nitrite reductase from the extremophile bacterium Thiolkalivibrio nitratireducens


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6278The drop contained 5mkl of enzyme solution (14.5 mg/ml) in 0.005 M Tris-borat buffer (pH 8.7) and 5 mkl reservoir solution. The reservoir solution contained 26.3% MPD, 0.175 M ammonium acetate in 0.09 M sodium citrate buffer (pH 5.6), VAPOR DIFFUSION, HANGING DROP, temperature 278K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 193.917α = 90
b = 193.917β = 90
c = 193.917γ = 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 BW7A0.96, 1.7375EMBL/DESY, HAMBURGBW7A

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
11.53097.40.03617.137379117.1
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)
1.51.5298.30.47612460

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.524.04373155112951000.1270.1260.12790.1410.1424RANDOM15.294
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_deg36.138
r_dihedral_angle_4_deg17.981
r_dihedral_angle_3_deg12.279
r_sphericity_free7.897
r_dihedral_angle_1_deg6.143
r_sphericity_bonded3.902
r_scangle_it3.561
r_scbond_it2.685
r_mcangle_it1.903
r_angle_refined_deg1.575
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.138
r_dihedral_angle_4_deg17.981
r_dihedral_angle_3_deg12.279
r_sphericity_free7.897
r_dihedral_angle_1_deg6.143
r_sphericity_bonded3.902
r_scangle_it3.561
r_scbond_it2.685
r_mcangle_it1.903
r_angle_refined_deg1.575
r_rigid_bond_restr1.423
r_mcbond_it1.377
r_angle_other_deg1.093
r_mcbond_other0.692
r_symmetry_vdw_other0.303
r_nbd_refined0.222
r_nbd_other0.204
r_nbtor_refined0.192
r_symmetry_hbond_refined0.191
r_symmetry_vdw_refined0.141
r_xyhbond_nbd_refined0.139
r_chiral_restr0.096
r_nbtor_other0.09
r_metal_ion_refined0.032
r_bond_refined_d0.019
r_gen_planes_refined0.015
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8228
Nucleic Acid Atoms
Solvent Atoms1217
Heterogen Atoms759

Software

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