3IR4
1.2 Angstrom Crystal Structure of the Glutaredoxin 2 (grxB) from Salmonella typhimurium in complex with Glutathione
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 295 | Protein solution: 0.3M Sodium chloride, 10mM HEPES (pH 7.5); Screen solution: 0.1M Sodium citrate (pH 5.6), 2M Ammonium sulphate, 0.2M Sodium-Potassium tartrate, 5mM Glutathione, 4% (w/v) Sucrose; Cryo solution: paratone, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.12 | 42.05 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.24 | α = 90 |
b = 58.76 | β = 90 |
c = 87.93 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 100 | CCD | MARMOSAIC 300 mm CCD | Mirrors | 2009-08-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.07810 | APS | 21-ID-D |
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 | 1.2 | 30 | 98.7 | 0.079 | 14.93 | 5.73 | 66655 | 66655 | -3 | 6.7 |
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 | 1.2 | 1.22 | 96.7 | 0.496 | 4.04 | 5.46 | 3133 |
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 | SAD | THROUGHOUT | 1.2 | 27.87 | 63340 | 63340 | 3315 | 98.65 | 0.11808 | 0.11808 | 0.11671 | 0.14426 | RANDOM | 6.29 |
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] | |
-0.28 | 0.15 | 0.14 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.367 |
r_dihedral_angle_4_deg | 13.454 |
r_dihedral_angle_3_deg | 10.531 |
r_dihedral_angle_1_deg | 4.801 |
r_scangle_it | 4.689 |
r_scbond_it | 3.281 |
r_mcangle_it | 2.032 |
r_rigid_bond_restr | 1.62 |
r_angle_refined_deg | 1.502 |
r_mcbond_it | 1.449 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1740 |
Nucleic Acid Atoms | |
Solvent Atoms | 489 |
Heterogen Atoms | 36 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
CRANK | phasing |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |