2F3U
Crystal Structure of the glycogen phosphorylase B / N-(beta-D-glucopyranosyl)-N'-cyclopropyl oxalamide complex
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, 3 mM DDT, pH 6.7, SMALL TUBES, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 49.59 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 127.957 | α = 90 |
b = 127.957 | β = 90 |
c = 116.03 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 | 293 | CCD | ADSC QUANTUM 4 | 2005-01-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X13 | 0.8034 | EMBL/DESY, HAMBURG | X13 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.93 | 30 | 99.3 | 0.059 | 6.6 | 4 | 72265 | 72265 | -3 | 27.9 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.93 | 1.96 | 99.1 | 0.38 | 1.9 | 4 | 3554 |
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 | THROUGHOUT | pdb entry 2PRJ | 1.93 | 30 | 72158 | 72158 | 3668 | 0.2 | 0.2 | 0.1908 | 0.2105 | RANDOM |
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] | |
-3.487 | -3.487 | 6.973 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 25.2 |
c_angle_deg | 1.24 |
c_improper_angle_d | 0.69 |
c_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6589 |
Nucleic Acid Atoms | |
Solvent Atoms | 300 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | refinement |
CNS | phasing |