4Q0G
Crystal structure of beta subunit of acyl-CoA carboxylase AccD1 from Mycobacterium tuberculosis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3U9R |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 0.1 M sodium HEPES pH 7.5 and 30% PEG300, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.88 | 68.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 142.571 | α = 90 |
b = 221.253 | β = 90 |
c = 167.835 | 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 | 110 | CCD | RAYONIX MX300HE | vertical focusing mirror: ultra-low expansion titanium silicate flat mirror with Pt, uncoated, and Pd strips. | 2011-06-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | 0.97949 | CLSI | 08ID-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 | 2.3 | 48.81 | 99.7 | 0.157 | 12.93 | 5.8 | 116259 | 115910 | -3 |
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 | 2.3 | 2.38 | 100 | 0.817 | 2.66 | 5.7 | 11512 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Number Reflections (All) | 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 | 3U9R | 2.31 | 48.81 | -3 | 110352 | 110021 | 5807 | 99.32 | 0.19044 | 0.18925 | 0.21325 | RANDOM | 27.757 |
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] | |
2.54 | -1.67 | -0.87 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.836 |
r_dihedral_angle_3_deg | 14.32 |
r_dihedral_angle_4_deg | 14.269 |
r_dihedral_angle_1_deg | 5.333 |
r_long_range_B_refined | 2.799 |
r_long_range_B_other | 2.799 |
r_scangle_other | 1.416 |
r_mcangle_it | 1.334 |
r_mcangle_other | 1.334 |
r_angle_refined_deg | 1.015 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11687 |
Nucleic Acid Atoms | |
Solvent Atoms | 573 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
MxDC | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |