3G12
Crystal structure of a putative lactoylglutathione lyase from Bdellovibrio bacteriovorus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 294 | 100mM Bis-tris pH 6.5, 2M Ammonium sulfate, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.11 | 41.65 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 91.276 | α = 90 |
b = 91.276 | β = 90 |
c = 57.711 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 | 90 | CCD | MAR CCD 165 mm | 2007-10-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.9793 | APS | 31-ID |
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 | 2.55 | 50 | 99.8 | 0.106 | 5.4 | 4.5 | 8394 | -5 | 49.658 |
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) | |||||||||||
2.55 | 2.64 | 99.5 | 0.661 | 1.5 | 3.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 2.58 | 20 | 7830 | 231 | 99.94 | 0.21392 | 0.21211 | 0.27481 | RANDOM | 45.277 |
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] | |
0.59 | 0.59 | -1.18 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.451 |
r_dihedral_angle_3_deg | 16.975 |
r_dihedral_angle_4_deg | 15.905 |
r_scangle_it | 8.419 |
r_dihedral_angle_1_deg | 6.061 |
r_scbond_it | 5.504 |
r_mcangle_it | 4.328 |
r_mcbond_it | 2.45 |
r_angle_refined_deg | 1.219 |
r_nbtor_refined | 0.294 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1740 |
Nucleic Acid Atoms | |
Solvent Atoms | 30 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
SHELXD | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |