3TQJ

Structure of the superoxide dismutase (Fe) (sodB) from Coxiella burnetii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ISAPDB CODE 1ISA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82980.1 M imidazole, 10% PEG 8000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.244.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.102α = 90
b = 65.285β = 90
c = 110.069γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442011-01-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
1210093.20.06634.213.52977727752-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0371.10.2514.13.61456

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 CODE 1ISA2.00456.152979127134138891.080.234940.233010.27066RANDOM25.616
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]
-0.94-0.81.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.057
r_dihedral_angle_3_deg12.338
r_dihedral_angle_4_deg9.019
r_dihedral_angle_1_deg5.18
r_scangle_it0.974
r_angle_refined_deg0.879
r_angle_other_deg0.786
r_scbond_it0.602
r_mcangle_it0.359
r_mcbond_it0.186
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.057
r_dihedral_angle_3_deg12.338
r_dihedral_angle_4_deg9.019
r_dihedral_angle_1_deg5.18
r_scangle_it0.974
r_angle_refined_deg0.879
r_angle_other_deg0.786
r_scbond_it0.602
r_mcangle_it0.359
r_mcbond_it0.186
r_chiral_restr0.055
r_mcbond_other0.035
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3134
Nucleic Acid Atoms
Solvent Atoms382
Heterogen Atoms2

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling