2GMU
Crystal structure of E coli GDP-4-keto-6-deoxy-D-mannose-3-dehydratase complexed with PLP-glutamate ketimine intermediate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2GMS | PDB ENTRY 2GMS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | batch | 6 | 298 | 14% PEG 3400, 0.05 M MES, 0.2 M MgCl2, 0.1 M NaCl, 1 mM pyridoxal-5-phosphate, 2 mM glutamate, 2 mM GDP, pH 6.0, batch, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.34 | 47.44 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.9 | α = 90 |
b = 88 | β = 90 |
c = 126 | 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 | 277 | AREA DETECTOR | SIEMENS HI-STAR | supper mirrors | 2005-10-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.9 | 30 | 88 | 0.0546 | 11.3 | 3.1 | 72854 | 72854 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.9 | 1.99 | 79 | 0.31 | 1.3 | 1.4 | 7334 |
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 | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 2GMS | 1.9 | 30 | 61081 | 61081 | 6079 | 88 | 0.176 | 0.176 | 0.174 | 0.231 | random |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_angle_deg | 2.6 |
t_bond_d | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6255 |
Nucleic Acid Atoms | |
Solvent Atoms | 295 |
Heterogen Atoms | 51 |
Software
Software | |
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Software Name | Purpose |
FRAMBO | data collection |
XDS | data reduction |
PHASER | phasing |
TNT | refinement |
XDS | data scaling |