3TZW

Crystal structure of a fragment containing the acyltransferase domain of Pks13 from Mycobacterium tuberculosis in the orthorhombic apoform at 2.6 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 DROP6.252930.1M KH2PO4/K2HPO4, 1.3M ammonium sulfate, 10mM malonate, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
358.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.659α = 90
b = 119.806β = 90
c = 50.162γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2007-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9395ESRFID14-4

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
12.64599.60.1063.8207412074143
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)
12.62.799.90.3681.6

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 2HG42.642.571969219692101699.370.190360.190360.186710.26392RANDOM27.284
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]
-1.17-1.12.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.921
r_dihedral_angle_4_deg19.845
r_dihedral_angle_3_deg19.552
r_dihedral_angle_1_deg7.373
r_scangle_it5.222
r_scbond_it3.224
r_angle_refined_deg2.147
r_mcangle_it2.111
r_mcbond_it1.141
r_chiral_restr0.139
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.921
r_dihedral_angle_4_deg19.845
r_dihedral_angle_3_deg19.552
r_dihedral_angle_1_deg7.373
r_scangle_it5.222
r_scbond_it3.224
r_angle_refined_deg2.147
r_mcangle_it2.111
r_mcbond_it1.141
r_chiral_restr0.139
r_bond_refined_d0.024
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3527
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms50

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling