4KXW
Human transketolase in covalent complex with donor ketose D-xylulose-5-phosphate, crystal 2
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 | 279 | 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 |
2.13 | 42.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 113.756 | α = 90 |
b = 86.017 | β = 125.46 |
c = 72.994 | 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 | CCD | ADSC QUANTUM 315r | mirrors | 2011-11-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 0.93939 | ESRF | ID14-4 |
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 | 0.97 | 30 | 92.5 | 0.047 | 14.23 | 3.3 | 312019 | 305775 | -3 | 10.555 |
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 | 0.97 | 1.04 | 78.2 | 0.437 | 2.74 |
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 | 0.97 | 30 | 305775 | 305775 | 6241 | 92.6 | 0.0987 | 0.0952 | 0.0952 | 0.121 | RANDOM | 15.9484 |
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 | 311 |
s_zero_chiral_vol | 6 |
s_non_zero_chiral_vol | 6 |
s_approx_iso_adps | 0.132 |
s_anti_bump_dis_restr | 0.11 |
s_rigid_bond_adp_cmpnt | 0.022 |
s_bond_d | 0.014 |
s_similar_dist | |
s_from_restr_planes | |
s_similar_adp_cmpnt |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4752 |
Nucleic Acid Atoms | |
Solvent Atoms | 963 |
Heterogen Atoms | 100 |
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 |