5SXT

Crystal structure of the S324T variant of Burkholderia pseudomallei KatG with isonicotinic acid hydrazide bound


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29316-20% PEG 4000, 20% MPD, 25 mM NaCl, 0.1 M sodium citrate pH 5.6
Crystal Properties
Matthews coefficientSolvent content
3.0860.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.22α = 90
b = 112.6β = 90
c = 173.7γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2009-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

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
11.994.481000.2424.86.6154729
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)
11.921000.91.86.522408

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 REPLACEMENTTHROUGHOUT1MWV1.920147102762699.940.1840.18230.2165RANDOM26.195
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]
0.58-0.2-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.436
r_dihedral_angle_4_deg17.312
r_dihedral_angle_3_deg13.774
r_dihedral_angle_1_deg6.057
r_mcangle_it2.44
r_angle_refined_deg2.056
r_mcbond_it1.63
r_mcbond_other1.628
r_angle_other_deg1.203
r_chiral_restr0.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.436
r_dihedral_angle_4_deg17.312
r_dihedral_angle_3_deg13.774
r_dihedral_angle_1_deg6.057
r_mcangle_it2.44
r_angle_refined_deg2.056
r_mcbond_it1.63
r_mcbond_other1.628
r_angle_other_deg1.203
r_chiral_restr0.144
r_bond_refined_d0.025
r_gen_planes_refined0.014
r_gen_planes_other0.009
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11010
Nucleic Acid Atoms
Solvent Atoms1232
Heterogen Atoms142

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing