4Z04
Crystal structure of a probable lactoylglutathione lyase from Brucella melitensis in complex with glutathione
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4QB5 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 290 | Molecular Dimensions, Morpheus e4: 30mM each: Di-Ethyleneglycol, Tri-Ethyleneglycol, TetraEthyleneglycol, Penta-Ethyleneglycol; 100mM Imidazole/MES pH 6.5; 12.5% each MPD (racemic), PEG 1K, PEG 3350; BrabA.17481.b.B1.PS02324 at 21.7mg/ml with 8mM Gluathione; Cryo: direct; tray 261781e4; puck epp4-1 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.11 | 41.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 82.63 | α = 90 |
b = 39.5 | β = 116.29 |
c = 41.7 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | RAYONIX MX-225 | 2015-03-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.45 | 50 | 98.4 | 0.034 | 0.04 | 20.5 | 3.96 | 21619 | 21264 | -3 | 15.47 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.45 | 1.49 | 89.1 | 0.308 | 0.383 | 2.97 | 2.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | FREE R-VALUE | 4QB5 | 1.45 | 20.622 | 1.35 | 21256 | 1082 | 98.67 | 0.1351 | 0.1337 | 0.1611 | Random selectiob | 25.2326 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.687 |
f_angle_d | 1.02 |
f_chiral_restr | 0.066 |
f_bond_d | 0.006 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 933 |
Nucleic Acid Atoms | |
Solvent Atoms | 122 |
Heterogen Atoms | 37 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |
BALBES | phasing |
PHENIX | model building |
Coot | model building |
PHENIX | refinement |
PDB_EXTRACT | data extraction |