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) | |||
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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 | 25% 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 | |
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Matthews coefficient | Solvent content |
2.64 | 53.41 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 103.95 | ¦Á = 90 |
b = 146.138 | ¦Â = 90 |
c = 174.749 | ¦Ã = 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 | 2021-07-15 | 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 | 1.553 | 87.374 | 89.4 | 0.114 | 0.035 | 0.999 | 10.1 | 11.4 | 100209 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.553 | 1.752 | 60.9 | 1.537 | 0.473 | 0.644 | 1.9 |
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 | 1.553 | 87.374 | 100208 | 5011 | 52.676 | 0.161 | 0.1595 | 0.1936 | 20.939 |
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] | |
-0.347 | 0.443 | -0.095 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.944 |
r_dihedral_angle_4_deg | 18.798 |
r_dihedral_angle_3_deg | 13.156 |
r_dihedral_angle_1_deg | 6.879 |
r_lrange_it | 4.685 |
r_lrange_other | 4.494 |
r_scangle_it | 2.96 |
r_scangle_other | 2.96 |
r_scbond_it | 1.944 |
r_scbond_other | 1.944 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8602 |
Nucleic Acid Atoms | |
Solvent Atoms | 1017 |
Heterogen Atoms | 163 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
autoPROC | data reduction |
STARANISO | data scaling |
MoRDa | phasing |