3QXI
Crystal structure of enoyl-CoA hydratase EchA1 from Mycobacterium marinum
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2IEX | PDB ENTRY 2IEX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 289 | MymaA.01530.f.A1 PS00846 at 33.15 mg/mL against JCSG+ A5, 0.2 M magnesium formate, 25% PEG 3350 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 218651a5, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.29 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 126.78 | α = 90 |
b = 77.71 | β = 107.94 |
c = 76.47 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | CCD | ADSC QUANTUM 315r | 2010-12-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | ALS | 5.0.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.2 | 50 | 96.9 | 0.08 | 14.4 | 3.7 | 36052 | 34932 | -3 | 30.815 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.2 | 2.26 | 82 | 0.412 | 2.83 | 3.3 | 2672 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2IEX | 2.2 | 50 | 34879 | 1735 | 96.86 | 0.1768 | 0.1736 | 0.237 | RANDOM | 25.579 |
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] | |
1.82 | 0.2 | 0.28 | -1.98 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.33 |
r_dihedral_angle_4_deg | 20.629 |
r_dihedral_angle_3_deg | 13.698 |
r_dihedral_angle_1_deg | 5.675 |
r_scangle_it | 3.505 |
r_scbond_it | 2.072 |
r_angle_refined_deg | 1.441 |
r_mcangle_it | 1.181 |
r_mcbond_it | 0.652 |
r_chiral_restr | 0.092 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5332 |
Nucleic Acid Atoms | |
Solvent Atoms | 398 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
BOS | data collection |
XDS | data reduction |