7PT4

Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) structure in complex with a covalently bound reaction intermediate as well as products formyl-CoA and acetone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4RJI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2932 M ammonium sulfate, 0.1 M HEPES pH 7.0 1 mM 2-Hydroxyisobutyryl-CoA, 5 mM ADP, 5 mM MgCl2, 5 mM ThDP
Crystal Properties
Matthews coefficientSolvent content
2.3347.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.234α = 90
b = 116.234β = 90
c = 312.056γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-03-11MSINGLE 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
11.64100.66296.80.1890.030.99915.340.198153
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)
11.641.8482.51.5390.2490.8781.738.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4RJI1.64100.66298152484164.5160.1470.14520.175119.878
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]
0.020.010.02-0.064
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.622
r_dihedral_angle_4_deg19.258
r_dihedral_angle_3_deg12.047
r_dihedral_angle_1_deg6.55
r_lrange_it6.071
r_lrange_other5.819
r_scangle_it3.537
r_scangle_other3.389
r_scbond_it2.538
r_scbond_other2.417
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.622
r_dihedral_angle_4_deg19.258
r_dihedral_angle_3_deg12.047
r_dihedral_angle_1_deg6.55
r_lrange_it6.071
r_lrange_other5.819
r_scangle_it3.537
r_scangle_other3.389
r_scbond_it2.538
r_scbond_other2.417
r_mcangle_it1.847
r_mcangle_other1.847
r_angle_refined_deg1.759
r_angle_other_deg1.485
r_mcbond_it1.212
r_mcbond_other1.209
r_nbd_refined0.215
r_symmetry_nbd_other0.185
r_symmetry_xyhbond_nbd_other0.184
r_xyhbond_nbd_refined0.183
r_symmetry_nbd_refined0.169
r_nbd_other0.167
r_nbtor_refined0.161
r_symmetry_xyhbond_nbd_refined0.14
r_chiral_restr0.088
r_symmetry_nbtor_other0.085
r_ncsr_local_group_10.076
r_metal_ion_refined0.026
r_bond_refined_d0.014
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 Atoms8730
Nucleic Acid Atoms
Solvent Atoms1049
Heterogen Atoms255

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
STARANISOdata scaling
MoRDaphasing