8VZB

Crystal Structure of 2-Hydroxacyl-CoA Lyase/Synthase ApbHACS from Alphaproteobacteria bacterium in the Complex with THDP, D-Lactyl-CoA, and ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2890.2 M ammonium phosphate dibasic, 20 % (w/v) PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.5451.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.709α = 90
b = 178.005β = 90
c = 196.111γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.0328APS23-ID-B

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
11.98131.8197.30.2750.30.1180.9957.81216596425.74
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)
11.982.0383.92.0392.3741.1850.4350.97.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.9847.271.35164990817596.610.1810.17910.218126.75
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.1068
f_angle_d0.741
f_chiral_restr0.0458
f_plane_restr0.0052
f_bond_d0.0029
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16712
Nucleic Acid Atoms
Solvent Atoms1477
Heterogen Atoms530

Software

Software
Software NamePurpose
PHENIXrefinement
autoPROCdata processing
XDSdata scaling
HKL-3000phasing
MOLREPphasing