1HLF
BINDING OF GLUCOPYRANOSYLIDENE-SPIRO-THIOHYDANTOIN TO GLYCOGEN PHOSPHORYLASE B: KINETIC AND CRYSTALLOGRAPHIC STUD
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 | CRYSTALLIZATION CONDITIONS: T-STATE GPB CRYSTALS (OIKONOMAKOS ET AL., 1985, BBA 832, 248) WERE SOAKED FOR 1 H IN A BUFFERED SOLUTION [10 MM BES, 0.1 MM EDTA, PH 6.7] CONTAINING A 70 MM CONCENTRATION OF THE COMPOUND, pH 6.70, SMALL TUBES, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.47 | 48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 128.787 | α = 90 |
b = 128.787 | β = 90 |
c = 116.169 | 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 | 298 | IMAGE PLATE | RIGAKU RAXIS IV | 1996-06-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R | 1.5418 |
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 | 2.26 | 28.06 | 97.4 | 0.041 | 3.8 | 45104 |
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) | |||||||||||
1 | 2.26 | 2.3 | 99.9 | 0.158 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | OTHER | THROUGHOUT | 2PRJ | 2.26 | 28.06 | 45104 | 2278 | 97.4 | 0.193 | 0.193 | 0.221 | 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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 25.4 |
x_angle_deg | 1.4 |
x_improper_angle_d | 0.75 |
x_bond_d | 0.008 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d | |
x_angle_d_na | |
x_angle_d_prot | |
x_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6749 |
Nucleic Acid Atoms | |
Solvent Atoms | 243 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
CCP4 | model building |
X-PLOR | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
CCP4 | phasing |