6C4Q

1.16 Angstrom Resolution Crystal Structure of Acyl Carrier Protein Domain (residues 1-100) of Polyketide Synthase Pks13 from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.3293Protein: 10.4 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen: AmSO4 (H8) 3.0M Ammonium sulfate, 1% (w/v) MPD. Cryo: Screen + 25% Ethylene Glycol
Crystal Properties
Matthews coefficientSolvent content
2.2344.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.889α = 90
b = 51.889β = 90
c = 74.427γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2017-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.163099.90.0920.0920.0960.02837.411.535889-310.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.161.181000.8080.8080.8550.2760.7982.89.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.1626.1334027179399.840.130290.129520.14456RANDOM16.387
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]
-0.11-0.110.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.069
r_dihedral_angle_4_deg18.316
r_sphericity_free13.793
r_rigid_bond_restr11.523
r_dihedral_angle_3_deg9.877
r_sphericity_bonded7.746
r_dihedral_angle_1_deg4.216
r_long_range_B_refined2.892
r_long_range_B_other2.605
r_scangle_other2.121
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.069
r_dihedral_angle_4_deg18.316
r_sphericity_free13.793
r_rigid_bond_restr11.523
r_dihedral_angle_3_deg9.877
r_sphericity_bonded7.746
r_dihedral_angle_1_deg4.216
r_long_range_B_refined2.892
r_long_range_B_other2.605
r_scangle_other2.121
r_scbond_it1.835
r_scbond_other1.834
r_mcangle_it1.578
r_mcangle_other1.577
r_angle_refined_deg1.392
r_mcbond_it1.13
r_mcbond_other1.13
r_angle_other_deg0.847
r_chiral_restr0.093
r_gen_planes_refined0.025
r_gen_planes_other0.021
r_bond_refined_d0.009
r_bond_other_d0.001
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms634
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing