3NZT
2.0 Angstrom Crystal structure of Glutamate--Cysteine Ligase (gshA) ftom Francisella tularensis in Complex with AMP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2D32 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 295 | protein: 7.3 mg/mL, 0.5M Sodium chloride, Tris-HCl (pH 8.3), 1mM AMPPNP, 1mM Magnesium chloride, screen: ClassicsII, drop A2, 0.1M Sodium acetate (pH 4.5), 2M Ammonium sulphate, Cryo: 1.8M Ammonium sulphate, 25% Sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.96 | 58.38 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.849 | α = 90 |
b = 89.849 | β = 90 |
c = 151.468 | γ = 120 |
Symmetry | |
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Space Group | P 65 |
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 225 mm CCD | Beryllium lenses | 2010-03-08 | 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) | 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 | 30 | 100 | 0.063 | 25.2 | 5.7 | 46618 | 46618 | -3 | 30.3 |
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 | 2.03 | 100 | 0.468 | 3.9 | 5.7 | 2296 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2D32 | 2 | 29.41 | 44206 | 44206 | 2351 | 99.93 | 0.16548 | 0.16548 | 0.1639 | 0.19598 | RANDOM | 29.23 |
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] | |
0.84 | 0.42 | 0.84 | -1.26 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.071 |
r_dihedral_angle_4_deg | 17.779 |
r_dihedral_angle_3_deg | 10.48 |
r_scangle_it | 4.324 |
r_dihedral_angle_1_deg | 3.149 |
r_scbond_it | 2.674 |
r_mcangle_it | 1.564 |
r_angle_refined_deg | 1.372 |
r_mcbond_it | 0.852 |
r_angle_other_deg | 0.848 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3977 |
Nucleic Acid Atoms | |
Solvent Atoms | 328 |
Heterogen Atoms | 78 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |