2QN3
Glycogen Phosphorylase in complex with N-4-chlorobenzoyl-N-beta-D-glucopyranosyl urea
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2PRJ | pdb entry 2PRJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | SMALL TUBES | 6.7 | 289 | 10 mM Bes, 3 mM DDT, pH 6.7, SMALL TUBES, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.48 | 50.37 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 128.841 | α = 90 |
b = 128.841 | β = 90 |
c = 116.486 | 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 | 2006-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX9.6 | 0.912 | SRS | PX9.6 |
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 | 1.95 | 99 | 97.9 | 0.046 | 20.1 | 5.2 | 70275 | 70275 | -3 | 25 |
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) | |||||||||||
1.95 | 1.99 | 93.1 | 0.318 | 4.3 | 5.3 | 3280 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | pdb entry 2PRJ | 1.96 | 91.29 | 66980 | 66980 | 3563 | 99.82 | 0.1858 | 0.18469 | 0.2064 | RANDOM | 27.235 |
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] | |
0.63 | 0.63 | -1.26 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.119 |
r_dihedral_angle_4_deg | 19.562 |
r_dihedral_angle_3_deg | 14.679 |
r_dihedral_angle_1_deg | 5.096 |
r_scangle_it | 1.931 |
r_scbond_it | 1.205 |
r_angle_refined_deg | 1.011 |
r_mcangle_it | 0.901 |
r_mcbond_it | 0.536 |
r_nbtor_refined | 0.301 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6632 |
Nucleic Acid Atoms | |
Solvent Atoms | 332 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |