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 | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 25% 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 | |
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Matthews coefficient | Solvent content |
2.54 | 51.67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 103.915 | α = 90 |
b = 146.718 | β = 90 |
c = 174.413 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | 2021-07-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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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 | 1.625 | 87.207 | 94.8 | 0.103 | 0.031 | 0.999 | 14.2 | 11.8 | 102472 |
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 | 1.625 | 1.78 | 1.624 | 0.481 | 0.686 | 1.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | FOURIER SYNTHESIS | FREE R-VALUE | 1.625 | 87.206 | 102471 | 5146 | 61.458 | 0.155 | 0.1537 | 0.1858 | 22.029 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.086 | 0.154 | -0.068 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.584 |
r_dihedral_angle_4_deg | 19.169 |
r_dihedral_angle_3_deg | 13.643 |
r_dihedral_angle_1_deg | 6.922 |
r_lrange_it | 4.944 |
r_lrange_other | 4.752 |
r_scangle_it | 3.108 |
r_scangle_other | 3.107 |
r_scbond_it | 2.046 |
r_scbond_other | 2.046 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8594 |
Nucleic Acid Atoms | |
Solvent Atoms | 969 |
Heterogen Atoms | 163 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
autoPROC | data reduction |
STARANISO | data scaling |
MOLREP | phasing |