4HDT
Crystal structure of a Carnitinyl-CoA dehydratase from Mycobacterium thermoresistibile
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5 | 290 | EMBioPACT screen A12: 10mM ZnCl2, 100mM NaOAc pH 5.0, 20% PEG 6000; MythA.01530.a.A1.PW28690 at 29mg/ml; 25% EG as cryo, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.2 | α = 90 |
b = 62.4 | β = 109.59 |
c = 56.88 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 2011-01-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 0.9774 | 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 | 1.6 | 50 | 98.9 | 0.053 | 16.77 | 3.8 | 42068 | 41586 | -3 | 22.954 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | Zn-SAD | THROUGHOUT | 1.6 | 45.45 | 42068 | 41568 | 2097 | 98.97 | 0.1611 | 0.1611 | 0.1597 | 0.1892 | RANDOM | 17.9527 |
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] | |
-0.32 | -0.38 | 0.38 | 0.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.848 |
r_dihedral_angle_4_deg | 13.054 |
r_dihedral_angle_3_deg | 11.393 |
r_dihedral_angle_1_deg | 5.831 |
r_angle_refined_deg | 1.526 |
r_angle_other_deg | 0.838 |
r_chiral_restr | 0.092 |
r_bond_refined_d | 0.013 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2488 |
Nucleic Acid Atoms | |
Solvent Atoms | 283 |
Heterogen Atoms | 10 |
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 |