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) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4RJI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 2 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 | |
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Matthews coefficient | Solvent content |
2.33 | 47.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 116.234 | α = 90 |
b = 116.234 | β = 90 |
c = 312.056 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER2 XE 16M | 2021-03-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9763 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||
1 | 1.64 | 100.662 | 96.8 | 0.189 | 0.03 | 0.999 | 15.3 | 40.1 | 98153 |
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) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.64 | 1.84 | 82.5 | 1.539 | 0.249 | 0.878 | 1.7 | 38.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 4RJI | 1.64 | 100.662 | 98152 | 4841 | 64.516 | 0.147 | 0.1452 | 0.1751 | 19.878 |
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] | |
0.02 | 0.01 | 0.02 | -0.064 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.622 |
r_dihedral_angle_4_deg | 19.258 |
r_dihedral_angle_3_deg | 12.047 |
r_dihedral_angle_1_deg | 6.55 |
r_lrange_it | 6.071 |
r_lrange_other | 5.819 |
r_scangle_it | 3.537 |
r_scangle_other | 3.389 |
r_scbond_it | 2.538 |
r_scbond_other | 2.417 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8730 |
Nucleic Acid Atoms | |
Solvent Atoms | 1049 |
Heterogen Atoms | 255 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
xia2 | data reduction |
STARANISO | data scaling |
MoRDa | phasing |