7ONF
The binding of p-coumaroyl glucose to glycogen phosphorylase reveals the relationship between structural data and effects on cell metabolome
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7O8E |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | SMALL TUBES | 6.8 | 289 | 10 mM BES buffer |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.48 | 50.31 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 128.607 | α = 90 |
b = 128.607 | β = 90 |
c = 116.633 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 298 | PIXEL | DECTRIS PILATUS 6M | 2019-05-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.9763 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.6 | 86.4 | 99.9 | 0.998 | 15.1 | 6.5 | 128346 | 28.2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.6 | 1.63 | 99.9 | 0.621 | 0.9 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 7O8E | 1.6 | 64.39 | 121187 | 6459 | 99.37 | 0.13014 | 0.12851 | 0.16112 | RANDOM | 36.348 |
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] | |
0.61 | 0.61 | -1.22 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.163 |
r_dihedral_angle_4_deg | 18.452 |
r_dihedral_angle_3_deg | 12.519 |
r_dihedral_angle_1_deg | 5.68 |
r_long_range_B_refined | 3.486 |
r_long_range_B_other | 3.288 |
r_scangle_other | 2.672 |
r_mcangle_it | 2.175 |
r_mcangle_other | 2.175 |
r_scbond_it | 2.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6589 |
Nucleic Acid Atoms | |
Solvent Atoms | 451 |
Heterogen Atoms | 61 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
REFMAC | phasing |