3QXZ
Crystal structure of a probable enoyl-CoA hydratase/isomerase from Mycobacterium abscessus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3GOW | PDB ENTRY 3GOW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 289 | MyabA.00358.c.A1 PS00900 at 53.9 mg/mL 3C cleaved against PACT screen condition H10, 0.2 M NaKHPO4, 0.1 M BisTris propane pH 6.5, 25% PEG3350 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 219606h10, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.46 | 50.08 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.17 | α = 90 |
b = 76.17 | β = 90 |
c = 122.52 | γ = 120 |
Symmetry | |
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Space Group | P 32 |
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 | 2011-02-10 | 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 | 1.35 | 50 | 99.9 | 0.055 | 15.11 | 4.5 | 174722 | 174539 | -3 | 18.15 |
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 | 1.35 | 1.39 | 99.8 | 0.49 | 2.9 | 4.1 | 13000 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3GOW | 1.35 | 50 | 174539 | 8736 | 99.89 | 0.1522 | 0.1514 | 0.16 | 0.1689 | 0.17 | RANDOM | 13.9098 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
0.04 | 0.02 | 0.04 | -0.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.841 |
r_dihedral_angle_4_deg | 17.536 |
r_dihedral_angle_3_deg | 11.169 |
r_dihedral_angle_1_deg | 5.453 |
r_scangle_it | 3.246 |
r_scbond_it | 1.994 |
r_angle_refined_deg | 1.372 |
r_mcangle_it | 1.239 |
r_mcbond_it | 0.707 |
r_chiral_restr | 0.082 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5592 |
Nucleic Acid Atoms | |
Solvent Atoms | 809 |
Heterogen Atoms | 70 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
BOS | data collection |
XDS | data reduction |