6T8E
Crystal structure of native xylose isomerase from Piromyces E2 grown in yeast, in complex with xylose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5NH5 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 294 | 14-17 % PEG3350, HEPES, pH 7 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.454 | α = 115.46 |
b = 79.267 | β = 89.99 |
c = 91.878 | γ = 117.07 |
Symmetry | |
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Space Group | P 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 | 110 | IMAGE PLATE | MARRESEARCH | 2018-08-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR-H | 1.54 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 1.86 | 46.6 | 93.6 | 0.066 | 0.09 | 0.06 | 0.931 | 7.1 | 2.1 | 135735 |
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) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.86 | 1.89 | 79.1 | 0.38 | 0.518 | 0.35 | 0.286 | 1.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | FOURIER SYNTHESIS | THROUGHOUT | 5NH5 | 1.86 | 46.6 | 128946 | 6788 | 93.61 | 0.1405 | 0.1386 | 0.1763 | RANDOM | 18.438 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
1.1 | 0.55 | -0.11 | -0.28 | -0.36 | -0.32 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.68 |
r_dihedral_angle_4_deg | 15.947 |
r_dihedral_angle_3_deg | 14.367 |
r_dihedral_angle_1_deg | 6.681 |
r_angle_refined_deg | 1.55 |
r_angle_other_deg | 1.443 |
r_chiral_restr | 0.079 |
r_bond_refined_d | 0.01 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13876 |
Nucleic Acid Atoms | |
Solvent Atoms | 1907 |
Heterogen Atoms | 263 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
REFMAC | phasing |