3PJ0
Crystal structure of a putative L-allo-threonine aldolase (lmo0305) from Listeria monocytogenes EGD-E at 1.80 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8.36 | 277 | 53.80% 2-methyl-2,4-pentanediol, 0.1M TRIS pH 8.36, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 85.593 | α = 90 |
b = 96.642 | β = 110.81 |
c = 99.478 | 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 | MAR MAR325 | 2010-05-13 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.96109,0.97915,0.97936 | SSRL | BL9-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.8 | 29.699 | 94.4 | 138522 | -3 | 16.78 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.8 | 1.86 | 95.3 | 0.371 | 1.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||||
X-RAY DIFFRACTION | MAD | 1.8 | 29.7 | 138490 | 6965 | 98.9 | 0.163 | 0.162 | 0.198 | 18.96 |
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] | |
-0.11 | -0.38 | 0.67 | -0.83 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.227 |
r_dihedral_angle_4_deg | 13.338 |
r_dihedral_angle_3_deg | 10.187 |
r_dihedral_angle_1_deg | 3.458 |
r_scangle_it | 2.962 |
r_scbond_it | 1.835 |
r_angle_refined_deg | 1.488 |
r_mcangle_it | 1.016 |
r_angle_other_deg | 0.931 |
r_mcbond_it | 0.59 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11243 |
Nucleic Acid Atoms | |
Solvent Atoms | 1522 |
Heterogen Atoms | 59 |
Software
Software | |
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Software Name | Purpose |
SOLVE | phasing |
REFMAC | refinement |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
qfit | model building |
XDS | data reduction |