3TZX

Crystal structure of a fragment containing the acyltransferase domain of Pks13 from Mycobacterium tuberculosis in tetragonal apo form at 2.3 A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HG4PDB ID: 2HG4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52850.1M HEPES, 1.7m ammonium sulfate, 15% glycerol, 1.7% PEG-400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties
Matthews coefficientSolvent content
3.3763.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.56α = 90
b = 106.56β = 90
c = 258.61γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102010-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.9334ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.341.796.90.0674.26509741.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.483.40.3292.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ID: 2HG42.341.126172761727329196.930.203190.203190.200170.26047RANDOM38.269
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]
1.051.05-2.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.517
r_dihedral_angle_4_deg21.991
r_dihedral_angle_3_deg17.301
r_dihedral_angle_1_deg6.883
r_angle_refined_deg2.068
r_chiral_restr0.132
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.517
r_dihedral_angle_4_deg21.991
r_dihedral_angle_3_deg17.301
r_dihedral_angle_1_deg6.883
r_angle_refined_deg2.068
r_chiral_restr0.132
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7123
Nucleic Acid Atoms
Solvent Atoms351
Heterogen Atoms44

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling