4U8G
Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Streptococcus agalactiae
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 20% polyethylene glycol monomethyl ether 550, 0.1 M sodium chloride, and 0.1 M sodium N,N-bis(2-hydroxyethyl)glycine (pH 9.0) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.08 | 60.01 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 83.943 | α = 90 |
b = 83.943 | β = 90 |
c = 181.101 | γ = 120 |
Symmetry | |
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Space Group | P 62 2 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 | 100 | CCD | ADSC QUANTUM 315 | 2011-02-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL38B1 | 1 | SPring-8 | BL38B1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.9 | 50 | 99.8 | 78.5 | 22.5 | 8964 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | THROUGHOUT | 3cxr | 2.9 | 35.64 | 8454 | 421 | 99.2 | 0.21477 | 0.21139 | 0.2869 | RANDOM | 75.396 |
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] | |
31.64 | 31.64 | -63.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.806 |
r_dihedral_angle_3_deg | 20.537 |
r_dihedral_angle_4_deg | 18.552 |
r_long_range_B_refined | 8.874 |
r_long_range_B_other | 8.873 |
r_dihedral_angle_1_deg | 6.056 |
r_mcangle_other | 5.633 |
r_mcangle_it | 5.626 |
r_scangle_other | 5.486 |
r_mcbond_it | 3.545 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1992 |
Nucleic Acid Atoms | |
Solvent Atoms | 5 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |