4UBV

Structure of the 3-ketoacyl-CoA thiolase FadA5 from M. tuberculosis with an partially acetylated cysteine in complex with acetyl-CoA and CoA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U1Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1 M Mes pH 6.5, 4% 1,4-dioxane, 1.8 M (NH4)2SO4
Crystal Properties
Matthews coefficientSolvent content
2.8657.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.68α = 90
b = 124.68β = 90
c = 124.71γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-05-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

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
11.9535.991000.13313.814.672009
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.951.991002.514.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1u1q1.9535.9968289364099.970.195030.193130.23074RANDOM29.824
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]
-2.04-2.044.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.511
r_dihedral_angle_4_deg22.038
r_dihedral_angle_3_deg15.064
r_dihedral_angle_1_deg7.772
r_angle_refined_deg1.358
r_chiral_restr0.116
r_gen_planes_refined0.022
r_bond_refined_d0.011
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.511
r_dihedral_angle_4_deg22.038
r_dihedral_angle_3_deg15.064
r_dihedral_angle_1_deg7.772
r_angle_refined_deg1.358
r_chiral_restr0.116
r_gen_planes_refined0.022
r_bond_refined_d0.011
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_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5814
Nucleic Acid Atoms
Solvent Atoms281
Heterogen Atoms276

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
iMOSFLMdata reduction
PHASERphasing