4ZOF

Lobenzarit-like inhibitor bound in the active site of Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (AnPRT; trpD)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QR9PDB entry 3QR9 chain A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52910.2 M imidazole-malate, 15% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.2745.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.191α = 90
b = 78.763β = 109.45
c = 99.674γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2014-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.9537Australian SynchrotronMX1

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
11.8471000.1797.37.563649-3

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEPDB entry 3QR9 chain A1.835.8091.3363643308399.970.18630.18460.2194Random selection
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_d12.246
f_angle_d1.098
f_chiral_restr0.041
f_bond_d0.01
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4868
Nucleic Acid Atoms
Solvent Atoms403
Heterogen Atoms104

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata scaling
Aimlessdata scaling
PHASERphasing
REFMACrefinement
Blu-Icedata collection