5SYJ

Crystal structure of the D141A variant of B. pseudomallei KatGin complex with isoniazid


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, 0.1 M sodium citrate pH 5.6
Crystal Properties
Matthews coefficientSolvent content
3.1761.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.64α = 90
b = 114.64β = 90
c = 174.99γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97949ALBAXALOC

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
11.8895.8998.40.06314.33.6155033
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)
11.881.9787.80.56231.572.917897

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 REPLACEMENTTHROUGHOUT1MWV1.8820155033816098.420.14180.14030.1703RANDOM28.742
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]
-0.010.22-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.778
r_dihedral_angle_4_deg17.149
r_dihedral_angle_3_deg13.077
r_dihedral_angle_1_deg6.074
r_mcangle_it3.018
r_angle_refined_deg2.296
r_mcbond_it2.234
r_mcbond_other2.231
r_angle_other_deg1.337
r_chiral_restr0.161
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.778
r_dihedral_angle_4_deg17.149
r_dihedral_angle_3_deg13.077
r_dihedral_angle_1_deg6.074
r_mcangle_it3.018
r_angle_refined_deg2.296
r_mcbond_it2.234
r_mcbond_other2.231
r_angle_other_deg1.337
r_chiral_restr0.161
r_bond_refined_d0.029
r_gen_planes_refined0.016
r_gen_planes_other0.01
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11004
Nucleic Acid Atoms
Solvent Atoms1159
Heterogen Atoms204

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing