9C1C | pdb_00009c1c

Mycobacterium tuberculosis PKS13 acyltransferase serine converted to beta-lactam form by CEC215 via SuFEx reaction


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3TZY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52900.1 M HEPES pH 7.5, 1.8 M (NH)4SO4, 4%-6% PEG400
Crystal Properties
Matthews coefficientSolvent content
2.346.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.524α = 90
b = 106.524β = 90
c = 258.644γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-04-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID1.0APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.055089.10.1430.1510.0450.9973.49.683855
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.122.1656.41.7892.1831.220.2442.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.2249.2570609277098.690.192190.190550.19750.235160.2364RANDOM47.584
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]
1.271.27-2.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.892
r_long_range_B_refined8.891
r_long_range_B_other8.887
r_dihedral_angle_2_deg8.681
r_scangle_other7.395
r_dihedral_angle_1_deg6.715
r_mcangle_other5.586
r_mcangle_it5.585
r_scbond_it5.167
r_scbond_other5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.892
r_long_range_B_refined8.891
r_long_range_B_other8.887
r_dihedral_angle_2_deg8.681
r_scangle_other7.395
r_dihedral_angle_1_deg6.715
r_mcangle_other5.586
r_mcangle_it5.585
r_scbond_it5.167
r_scbond_other5
r_mcbond_it3.837
r_mcbond_other3.835
r_angle_refined_deg1.657
r_angle_other_deg0.564
r_chiral_restr0.075
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7159
Nucleic Acid Atoms
Solvent Atoms316
Heterogen Atoms194

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXphasing