1R6W
Crystal structure of the K133R mutant of o-Succinylbenzoate synthase (OSBS) from Escherichia coli. Complex with SHCHC
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 5.5 | 293 | The K133R mutant of OSBS was concentrated to 15 mg/ml, dialyzed against 5 mM Tris pH 8.3 containing 2 mM MgCl2, drop frozen as small pellets in liquid nitrogen and stored at -80 C. Crystals were grown at 20 C by small-scale batch experiments by combining 15 ml of protein solution and 15 ml of a solution containing 12-13% MePEG 5000, 100 mM sodium acetate, 60 mM MgCl2, at pH 5.5. SHCHC was included in the crystallization at a final concentration of approximately 2.5 mM., microbatch, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.11 | 41.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 72.2 | α = 90 |
b = 82.9 | β = 90 |
c = 56.2 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | 150 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-BM-D | 0.9790 | APS | 14-BM-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 | 1.62 | 31 | 99.9 | 0.046 | 41 | 7.1 | 43694 | 43694 | 25.9 |
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) | |||||||||||
1.62 | 1.68 | 98.9 | 0.293 | 17.1 |
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 | 1fhv | 1.62 | 30 | 41456 | 41456 | 2190 | 99.82 | 0.16911 | 0.1691 | 0.16743 | 0.20024 | RANDOM | 17.89 |
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] | |
-0.58 | -1.38 | 1.96 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 6.573 |
r_scangle_it | 4.732 |
r_scbond_it | 3.057 |
r_mcangle_it | 2.162 |
r_angle_refined_deg | 1.615 |
r_angle_other_deg | 1.237 |
r_mcbond_it | 1.236 |
r_symmetry_vdw_refined | 0.31 |
r_symmetry_vdw_other | 0.287 |
r_nbd_other | 0.253 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2488 |
Nucleic Acid Atoms | |
Solvent Atoms | 344 |
Heterogen Atoms | 18 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SCALEPACK | data scaling |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |