6Y5C
The crystal structure of glycogen phosphorylase in complex with 52
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | SMALL TUBES | 6.7 | 289 | 10 mM BES buffer, pH 6.7 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 49.44 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 127.957 | α = 90 |
b = 127.957 | β = 90 |
c = 115.921 | 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 | 293 | CCD | AGILENT ATLAS CCD | 2018-05-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | OXFORD DIFFRACTION SUPERNOVA | 1.5419 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.4 | 13.68 | 91.2 | 0.101 | 0.988 | 10.7 | 4.8 | 34314 |
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 | 2.4 | 2.49 | 80.2 | 0.623 | 0.754 | 1.4 | 3.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.4 | 13.68 | 32625 | 1679 | 89.76 | 0.17035 | 0.16823 | 0.21117 | RANDOM | 27.009 |
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] | |
-0.17 | -0.17 | 0.34 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.772 |
r_dihedral_angle_4_deg | 19.6 |
r_dihedral_angle_3_deg | 15.344 |
r_long_range_B_refined | 6.397 |
r_dihedral_angle_1_deg | 6.172 |
r_scbond_it | 2.626 |
r_mcangle_it | 2.588 |
r_mcbond_it | 1.529 |
r_angle_refined_deg | 0.941 |
r_chiral_restr | 0.077 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6597 |
Nucleic Acid Atoms | |
Solvent Atoms | 244 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrysalisPro | data reduction |
Aimless | data scaling |
REFMAC | phasing |