1LBY
Crystal Structure of a complex (P32 crystal form) of dual activity FBPase/IMPase (AF2372) from Archaeoglobus fulgidus with 3 Manganese ions, Fructose-6-Phosphate, and Phosphate ion
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1DK4 | PDB ENTRY 1DK4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 298 | PEG 3350, ammonium nitrate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.23 | 70.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.25 | α = 90 |
b = 89.25 | β = 90 |
c = 102.97 | γ = 120 |
Symmetry | |
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Space Group | P 32 |
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 | 110 | CCD | RIGAKU JUPITER | Osmic Blue mirrors | 2001-12-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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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 | 2.25 | 40 | 96.7 | 0.133 | 5.5 | 2.2 | 41420 | 43100 |
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) | |||||||||||
2.25 | 2.33 | 96.3 | 0.4 | 1 | 2.1 | 4378 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1DK4 | 2.25 | 30 | 39564 | 39564 | 1648 | 96.1 | 0.154 | 0.154 | 0.152 | 0.17 | 0.21 | 0.17 | Every 25 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_non_zero_chiral_vol | 0.034 |
s_zero_chiral_vol | 0.027 |
s_angle_d | 0.022 |
s_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3932 |
Nucleic Acid Atoms | |
Solvent Atoms | 186 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
AMoRE | phasing |
SHELXL-97 | refinement |
CrystalClear | data reduction |
CrystalClear | data scaling |