3MT8
Glycogen phosphorylase complexed with 4-chlorobenzaldehyde-4-(beta-D-glucopyranosyl)-thiosemicarbazone
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2PRJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | SMALL TUBES | 6.7 | 289 | Crystals grown from 20 mg/ml protein in a buffer of 10 mM BES, pH 6.7, 1mM EDTA, 3mM DTT. Crystals soaked with 20mM inhibitor in 20% DMSO for 21 hrs, SMALL TUBES, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 49.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 128.15 | α = 90 |
b = 128.15 | β = 90 |
c = 115.97 | 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 | MARMOSAIC 225 mm CCD | 2007-11-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX10.1 | 1.04498 | SRS | PX10.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 35.69 | 97 | 0.054 | 21.3 | 5.4 | 63139 | 63139 | -3 | 27.4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2 | 2.11 | 97.1 | 0.221 | 7.2 | 5.4 | 9172 |
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 | 2PRJ | 2 | 35.69 | 59914 | 59914 | 3197 | 96.2 | 0.1945 | 0.19346 | 0.21418 | RANDOM | 31.102 |
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] | |
0.86 | 0.86 | -1.73 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.759 |
r_dihedral_angle_4_deg | 18.259 |
r_dihedral_angle_3_deg | 15.411 |
r_dihedral_angle_1_deg | 5.149 |
r_scangle_it | 2.04 |
r_scbond_it | 1.256 |
r_angle_refined_deg | 1.026 |
r_mcangle_it | 0.966 |
r_mcbond_it | 0.562 |
r_nbtor_refined | 0.304 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6604 |
Nucleic Acid Atoms | |
Solvent Atoms | 292 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CNS | refinement |
HKL-3000 | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | phasing |