6QV9

Staphylococcus aureus superoxide dismutase SodA double mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.15200 mM MgCl2, 100 mM Bis-Tris pH 5.5, 25% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.243.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.25α = 90
b = 68.15β = 100.58
c = 57.29γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I031.550DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.843.4699.40.99510.9636588
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8496.40.732.24

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 REPLACEMENTTHROUGHOUT6EX31.835.7734541173598.870.172520.170760.20685RANDOM21.466
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]
0.47-1.65-0.730.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.038
r_dihedral_angle_3_deg12.706
r_dihedral_angle_4_deg6.422
r_dihedral_angle_1_deg6.259
r_long_range_B_refined5.963
r_long_range_B_other5.961
r_scangle_other5.232
r_scbond_it3.249
r_scbond_other3.248
r_mcangle_it2.843
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.038
r_dihedral_angle_3_deg12.706
r_dihedral_angle_4_deg6.422
r_dihedral_angle_1_deg6.259
r_long_range_B_refined5.963
r_long_range_B_other5.961
r_scangle_other5.232
r_scbond_it3.249
r_scbond_other3.248
r_mcangle_it2.843
r_mcangle_other2.842
r_mcbond_it1.92
r_mcbond_other1.915
r_angle_refined_deg1.559
r_angle_other_deg1.475
r_chiral_restr0.086
r_bond_refined_d0.01
r_gen_planes_refined0.009
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3198
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms2

Software

Software
Software NamePurpose
GDAdata collection
xia2data reduction
XDSdata scaling
Aimlessdata scaling
MOLREPphasing
Cootmodel building
REFMACrefinement