1KER
The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-D-glucose bound
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1G1A | PDB 1G1A |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.4 | 293 | 30% w/v PEG 8000, 0.1M sodium cacodylate pH 5.4, 0.2M ammonium sulphate, VAPOR DIFFUSION, HANGING DROP at 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.45 | 64.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.225 | α = 90 |
b = 96.151 | β = 90 |
c = 182.888 | 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 | ADSC QUANTUM 4 | mirrors | 2001-06-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.933 | ESRF | BM14 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.2 | 49.7 | 99.8 | 0.134 | 0.112 | 5.7 | 3.2 | 55517 | 19.232 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.2 | 2.32 | 99.9 | 0.34 | 0.284 | 2.6 | 3.3 | 8000 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB 1G1A | 2.2 | 49.7 | 55421 | 5507 | 99.5 | 0.175 | 0.206 | Random | 17.17 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.1525 |
c_angle_deg | 1.2202 |
c_improper_angle_d | 0.7839 |
c_bond_d | 0.0053 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5488 |
Nucleic Acid Atoms | |
Solvent Atoms | 712 |
Heterogen Atoms | 175 |
Software
Software | |
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Software Name | Purpose |
AMoRE | phasing |
CNS | refinement |
MOSFLM | data reduction |
CCP4 | data scaling |