3SC6
2.65 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose reductase (rfbD) from Bacillus anthracis str. Ames in complex with NADP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1VL0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 297 | Protein: 7.5 mg/mL in buffer containing 10 mM Tris HCl pH 8.3, 500 mM NaCl, and 5 mM BME, 5 mM MgCl2, 1 mM NADP+, and 10% glycerol.Crystallization conditions: 0.2 M lithium sulfate, 0.1 M Tris pH 8.5, and 25% w/v PEG 5000 MME |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.32 | 62.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.449 | α = 90 |
b = 113.337 | β = 91.18 |
c = 144.949 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | Mirror | 2011-03-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 0.97856 | 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 | 2.65 | 30 | 100 | 0.102 | 11.49 | 3.8 | 75200 | 75200 | -3 | 67.1 |
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 | 2.65 | 2.7 | 100 | 0.615 | 2.35 | 3.8 | 3724 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1VL0 | 2.65 | 29.9 | 70861 | 70861 | 3745 | 99.94 | 0.21747 | 0.21531 | 0.25785 | RANDOM | 56.691 |
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] | |
4.94 | 0.53 | -0.35 | -4.56 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 9.937 |
r_dihedral_angle_4_deg | 4.542 |
r_dihedral_angle_3_deg | 4.01 |
r_scangle_it | 3.011 |
r_scbond_it | 1.822 |
r_angle_refined_deg | 1.359 |
r_mcangle_it | 1.172 |
r_angle_other_deg | 0.791 |
r_dihedral_angle_1_deg | 0.68 |
r_mcbond_it | 0.606 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13571 |
Nucleic Acid Atoms | |
Solvent Atoms | 240 |
Heterogen Atoms | 373 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |