7PT3

Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493A structure in complex with substrate 2-HIB-CoA and inactive cofactor 3-deaza-ThDP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29325% PEG 1500, 0.1 M SPG buffer pH 6.0, 5 mM 3-deaza-ThDP, 1 mM 2-hydroxybutyryl-CoA, 5 mM MgCl2, 5 mM ADP
Crystal Properties
Matthews coefficientSolvent content
2.5451.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.915α = 90
b = 146.718β = 90
c = 174.413γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.62587.20794.80.1030.0310.99914.211.8102472
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.6251.781.6240.4810.6861.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE1.62587.206102471514661.4580.1550.15370.185822.029
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]
-0.0860.154-0.068
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.584
r_dihedral_angle_4_deg19.169
r_dihedral_angle_3_deg13.643
r_dihedral_angle_1_deg6.922
r_lrange_it4.944
r_lrange_other4.752
r_scangle_it3.108
r_scangle_other3.107
r_scbond_it2.046
r_scbond_other2.046
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.584
r_dihedral_angle_4_deg19.169
r_dihedral_angle_3_deg13.643
r_dihedral_angle_1_deg6.922
r_lrange_it4.944
r_lrange_other4.752
r_scangle_it3.108
r_scangle_other3.107
r_scbond_it2.046
r_scbond_other2.046
r_mcangle_it1.931
r_mcangle_other1.931
r_angle_refined_deg1.778
r_angle_other_deg1.502
r_mcbond_it1.296
r_mcbond_other1.287
r_nbd_refined0.218
r_nbd_other0.194
r_symmetry_nbd_other0.183
r_symmetry_nbd_refined0.183
r_xyhbond_nbd_refined0.182
r_symmetry_xyhbond_nbd_refined0.174
r_nbtor_refined0.163
r_symmetry_xyhbond_nbd_other0.139
r_chiral_restr0.088
r_symmetry_nbtor_other0.085
r_ncsr_local_group_10.057
r_metal_ion_refined0.033
r_xyhbond_nbd_other0.015
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8594
Nucleic Acid Atoms
Solvent Atoms969
Heterogen Atoms163

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing