3SB0

Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 4-(2-chloro-6-fluoro-3-methylphenyl)-2,4-dioxobutanoic acid inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N8Ipdb entry 1N8I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829020% PEG 3350, 0.1 M magnesium chloride, 0.1 M TRIS-HCl , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.1442.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.534α = 90
b = 78.534β = 90
c = 224.07γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCD2 x 2 mosaic CCD detector2010-04-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97929APS19-ID

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
11.7345.60595.70.1916.211.6711676808622
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.731.767.5

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISpdb entry 1N8I2.19945.6051.347116736507182599.610.17470.17210.2231
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]
0.46870.4687-0.9375
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.989
f_angle_d1.062
f_chiral_restr0.069
f_bond_d0.008
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5418
Nucleic Acid Atoms
Solvent Atoms400
Heterogen Atoms20

Software

Software
Software NamePurpose
PHENIXrefinement
REFMACrefinement
PHENIXmodel building
BUSTERrefinement
HKL-3000data reduction
HKL-3000data scaling
REFMACphasing
PHENIXphasing
HKL-3000data collection