6HA3
Human transketolase variant E160Q in covalent complex with donor ketose D-fructose-6-phosphate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.9 | 277 | Reservoir mixture of 13.5-15 % PEG 6000 (w/v), 4% PEG 400 (v/v), 2 % glycerol (v/v) , pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 279.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.11 | 41.66 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 114.07 | α = 90 |
b = 86.09 | β = 125.22 |
c = 73.21 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | PIXEL | DECTRIS PILATUS 6M-F | 2015-11-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.85 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | 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 | 1.08 | 24.558 | 96.4 | 0.052 | 0.057 | 0.999 | 13.94 | 5.806 | 238255 | 11.37 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.08 | 1.15 | 94.4 | 0.677 | 0.743 | 0.783 | 2.43 | 5.826 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | THROUGHOUT | 1.08 | 24.558 | 1.35 | 238226 | 11910 | 96.66 | 0.1123 | 0.1114 | 0.1295 | 17.3492 |
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 |
f_dihedral_angle_d | 14.485 |
f_angle_d | 1.832 |
f_chiral_restr | 0.087 |
f_bond_d | 0.011 |
f_plane_restr | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4747 |
Nucleic Acid Atoms | |
Solvent Atoms | 682 |
Heterogen Atoms | 155 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHENIX | phasing |