6EP8

InhA Y158F mutant in complex with NADH from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4TRO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5287Thrombin cleaved InhA at 10 mg/ml with 3 to 10 mM of NADH was crystallized in a 24-well crystal plate, Combiclover Junior (Jena Bioscience). The best crystals appeared in drops of 2 ul of enzyme solution, 1 ul of the reservoir solution and 1 ul of distilled water. The reservoir solution contained 100 mM HEPES/NaOH pH 7.5, 50 mM sodium citrate pH 6.5, 7-9 % 2-methyl-2,4-pentanediol. Crystals appeared typically within two to three weeks in this condition.
Crystal Properties
Matthews coefficientSolvent content
3.362.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.273α = 90
b = 98.273β = 90
c = 139.836γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A1.07244ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.846.611000.0650.0670.015135.620.537644
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.91001.211.240.2710.9242.920.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4TRO1.842.5531.3437562188499.90.14680.14540.1751
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.166
f_angle_d1.129
f_chiral_restr0.061
f_bond_d0.009
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1995
Nucleic Acid Atoms
Solvent Atoms264
Heterogen Atoms92

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing