4GUH
1.95 Angstrom Crystal Structure of the Salmonella enterica 3-Dehydroquinate Dehydratase (aroD) E86A Mutant in Complex with Dehydroshikimate (Crystal Form #2)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 9 | 300 | protein: 7.5 mg/mL in 0.5 M sodium chloride, 0.01 M Tris-HCl, crystallization condition: Qiagen PEG B6 (0.1 M MIB buffer, pH 9.0, 25% w/v PEG1500), 25 mM dehydroquinic acid crystal soak, VAPOR DIFFUSION, SITTING DROP, temperature 300K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.89 | 34.81 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 36.838 | α = 90 |
b = 71.671 | β = 90 |
c = 171.755 | 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 | Beryllium lens | 2012-06-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97857 | APS | 21-ID-G |
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 | 1.95 | 30 | 99.9 | 0.081 | 3 | 7.1 | 34213 | 34213 | -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) | |||||||||||
1 | 1.95 | 1.98 | 99.9 | 0.611 | 3 | 6.9 | 1655 |
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 | PDB ENTRY 3L2I | 1.95 | 28.63 | 32362 | 32362 | 1746 | 99.82 | 0.19292 | 0.19292 | 0.18994 | 0.24735 | RANDOM | 34.952 |
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] | |
-1.11 | 4.4 | -3.29 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.046 |
r_dihedral_angle_4_deg | 14.069 |
r_dihedral_angle_3_deg | 10.691 |
r_dihedral_angle_1_deg | 3.152 |
r_angle_refined_deg | 1.437 |
r_angle_other_deg | 0.728 |
r_chiral_restr | 0.085 |
r_bond_refined_d | 0.01 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4002 |
Nucleic Acid Atoms | |
Solvent Atoms | 243 |
Heterogen Atoms | 23 |
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 |