3KHU
Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2Q3E | PDB entry 2Q3E |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277.15 | 18% PEG smears (PEG 400, 600, 1000, 2000, 3350, 4000, 5000 MME, 6000, 8000, 10000), 0.1M HEPES pH 7.5, 5% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.15 | 60.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 203.54 | α = 90 |
b = 207.34 | β = 90 |
c = 93.4 | 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 | 100 | CCD | ADSC QUANTUM 315 | mirrors | 2009-07-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9763 | Diamond | I03 |
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 | 2.3 | 48.74 | 99.8 | 0.106 | 9.4 | 4.3 | 175207 | 175139 | 2 |
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 | 2.3 | 2.42 | 100 | 0.743 | 2 | 4.3 | 25412 |
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 | PDB entry 2Q3E | 2.3 | 48.74 | 175128 | 173128 | 1988 | 99.71 | 0.19544 | 0.19509 | 0.2252 | RANDOM | 19.743 |
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] | |
-3.2 | 0.75 | 2.45 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.178 |
r_dihedral_angle_4_deg | 20.67 |
r_dihedral_angle_3_deg | 13.744 |
r_scangle_it | 7.651 |
r_scbond_it | 5.293 |
r_dihedral_angle_1_deg | 5.28 |
r_mcangle_it | 2.975 |
r_mcbond_it | 1.593 |
r_angle_refined_deg | 1.438 |
r_angle_other_deg | 1.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 21667 |
Nucleic Acid Atoms | |
Solvent Atoms | 1314 |
Heterogen Atoms | 515 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
PHASER | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |