7PT1

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29325% PEG 1500, 0.1 M MIB buffer (sodium malonate dibasic monohydrate, imidazole, boric acid) pH 6.0 5 mM 3-deazathiamin diphosphate, 1 mM 2-Hydroxyisobutyryl-CoA, 5 mM MgCl2, 5 mM ADP
Crystal Properties
Matthews coefficientSolvent content
2.6453.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.95α = 90
b = 146.138β = 90
c = 174.749γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-07-15MSINGLE 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
11.55387.37489.40.1140.0350.99910.111.4100209
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)
11.5531.75260.91.5370.4730.6441.9

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-VALUE4RJI1.55387.374100208501152.6760.1610.15950.193620.939
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]
-0.3470.443-0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.944
r_dihedral_angle_4_deg18.798
r_dihedral_angle_3_deg13.156
r_dihedral_angle_1_deg6.879
r_lrange_it4.685
r_lrange_other4.494
r_scangle_it2.96
r_scangle_other2.96
r_scbond_it1.944
r_scbond_other1.944
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.944
r_dihedral_angle_4_deg18.798
r_dihedral_angle_3_deg13.156
r_dihedral_angle_1_deg6.879
r_lrange_it4.685
r_lrange_other4.494
r_scangle_it2.96
r_scangle_other2.96
r_scbond_it1.944
r_scbond_other1.944
r_mcangle_other1.891
r_mcangle_it1.89
r_angle_refined_deg1.853
r_angle_other_deg1.514
r_mcbond_it1.257
r_mcbond_other1.255
r_nbd_refined0.218
r_symmetry_nbd_refined0.217
r_symmetry_xyhbond_nbd_refined0.193
r_nbd_other0.187
r_symmetry_nbd_other0.181
r_xyhbond_nbd_refined0.173
r_nbtor_refined0.163
r_symmetry_xyhbond_nbd_other0.12
r_chiral_restr0.095
r_symmetry_nbtor_other0.084
r_ncsr_local_group_10.059
r_xyhbond_nbd_other0.043
r_metal_ion_refined0.017
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8602
Nucleic Acid Atoms
Solvent Atoms1017
Heterogen Atoms163

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
STARANISOdata scaling
MoRDaphasing