2Q8M
T-like Fructose-1,6-bisphosphatase from Escherichia coli with AMP, Glucose 6-phosphate, and Fructose 1,6-bisphosphate bound
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2GQ1 | PDB ENTRY 2GQ1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 295 | Protein solution: (15 mg/mL enzyme (pH 7.4), 20 mM dithiothreitol (DTT), 0.1 mM EDTA, 5 mM Fru-1,6-P2, 5 mM MgCl2, and 5 mM AMP) Precipitant solution: (50 mM MES-NaOH, pH 6.5, 13% (w/v) PEG 10,000, and 20% (w/v) sucrose), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.45 | 64.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 124.64 | α = 90 |
b = 124.64 | β = 90 |
c = 132.28 | γ = 90 |
Symmetry | |
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Space Group | P 41 2 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 | 100 | CCD | NOIR-1 | 2005-01-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 4.2.2 | 0.979 | ALS | 4.2.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.05 | 39.41 | 96.6 | 0.068 | 0.068 | 9.2 | 2.43 | 63542 | 63542 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.05 | 2.12 | 95.7 | 0.255 | 0.255 | 3.5 | 2.47 | 6202 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2GQ1 | 2.05 | 37.77 | 63536 | 63536 | 6416 | 96.5 | 0.212 | 0.212 | 0.209 | 0.235 | RANDOM | 31.8 |
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] | |
-1.71 | -1.71 | 3.43 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.8 |
c_scangle_it | 3.24 |
c_scbond_it | 2.36 |
c_mcangle_it | 2.2 |
c_mcbond_it | 1.38 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.74 |
c_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4868 |
Nucleic Acid Atoms | |
Solvent Atoms | 312 |
Heterogen Atoms | 109 |
Software
Software | |
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Software Name | Purpose |
d*TREK | data processing |
CNS | refinement |
PDB_EXTRACT | data extraction |
CrystalClear | data collection |
d*TREK | data reduction |
d*TREK | data scaling |
AMoRE | phasing |