4KXY
Human transketolase in complex with ThDP analogue (R)-2-(1,2-dihydroxyethyl)-3-deaza-ThDP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3MOS | PDB ENTRY 3MOS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.9 | 293 | 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 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.14 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.15 | α = 90 |
b = 86.05 | β = 94.12 |
c = 92.73 | 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 225 mm CCD | mirrors | 2011-11-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.9841 | BESSY | 14.1 |
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 | 1.26 | 30 | 99.6 | 0.066 | 13.07 | 3.1 | 307778 | 307778 | -3 | 14.88 |
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 | 1.26 | 1.36 | 99.7 | 0.599 | 2.25 |
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 | FREE R | PDB ENTRY 3MOS | 1.26 | 30 | 307778 | 307778 | 17424 | 99.7 | 0.1651 | 0.1538 | 0.1538 | 0.2038 | RANDOM | 16.4439 |
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 |
s_angle_d | 318 |
s_similar_dist | 67 |
s_zero_chiral_vol | 51 |
s_non_zero_chiral_vol | 4 |
s_approx_iso_adps | 0.159 |
s_anti_bump_dis_restr | 0.058 |
s_bond_d | 0.012 |
s_rigid_bond_adp_cmpnt | 0.011 |
s_from_restr_planes | |
s_similar_adp_cmpnt |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9494 |
Nucleic Acid Atoms | |
Solvent Atoms | 1462 |
Heterogen Atoms | 182 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
SHELX | refinement |
PDB_EXTRACT | data extraction |
DNA | data collection |
XDS | data reduction |
PHENIX | phasing |
SHELXL | refinement |