3E3L
The R-state Glycogen Phosphorylase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 9GPB | pdb entry 9gpb |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | SMALL TUBES | 7.5 | 289 | 1.1-1.3 M ammonium sulfate, 10mM beta-glycerophosphate buffer pH 7.5, 0.5mM EDTA, SMALL TUBES, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.41 | 48.93 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 118.895 | α = 90 |
b = 189.92 | β = 109.27 |
c = 88.16 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 293 | CCD | MARMOSAIC 225 mm CCD | 2008-02-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX10.1 | 0.97976 | SRS | PX10.1 |
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 | 2.59 | 30 | 99.6 | 0.064 | 11.7 | 3.4 | 112937 | 107281 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.6 | 2.64 | 99.6 | 0.358 | 3.89 | 3.3 |
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 9gpb | 2.59 | 29.59 | 107281 | 107281 | 5654 | 99.29 | 0.20958 | 0.20656 | 0.26577 | RANDOM | 49.826 |
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] | |
-1.95 | -0.36 | 1.71 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.841 |
r_dihedral_angle_3_deg | 21.501 |
r_dihedral_angle_4_deg | 19.187 |
r_dihedral_angle_1_deg | 6.261 |
r_scangle_it | 1.889 |
r_angle_refined_deg | 1.341 |
r_scbond_it | 1.125 |
r_mcangle_it | 0.851 |
r_mcbond_it | 0.471 |
r_nbtor_refined | 0.312 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 26363 |
Nucleic Acid Atoms | |
Solvent Atoms | 110 |
Heterogen Atoms | 60 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MAR345 | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | phasing |