5SX1

Crystal structure of D141E variant of B. pseudomallei KatG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MWV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29316-20% MPD, pH 5.6 0.1 M sodium citrate
Crystal Properties
Matthews coefficientSolvent content
3.2261.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.739α = 90
b = 116.198β = 90
c = 175.018γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

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
11.896.8199.20.1089.35.7178948
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)
11.81.8594.90.4334.4

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 REPLACEMENTTHROUGHOUT1MWV1.820178948929299.080.15650.15480.1905RANDOM22.689
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]
0.160.55-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.141
r_dihedral_angle_4_deg16.999
r_dihedral_angle_3_deg12.816
r_dihedral_angle_1_deg6.062
r_mcangle_it2.91
r_angle_refined_deg2.393
r_mcbond_it2.037
r_mcbond_other2.017
r_angle_other_deg1.279
r_chiral_restr0.178
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.141
r_dihedral_angle_4_deg16.999
r_dihedral_angle_3_deg12.816
r_dihedral_angle_1_deg6.062
r_mcangle_it2.91
r_angle_refined_deg2.393
r_mcbond_it2.037
r_mcbond_other2.017
r_angle_other_deg1.279
r_chiral_restr0.178
r_bond_refined_d0.032
r_gen_planes_refined0.017
r_gen_planes_other0.011
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11012
Nucleic Acid Atoms
Solvent Atoms1597
Heterogen Atoms132

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing