5V2I
Crystal structure of a mutant glycosylasparaginase (G172D) that causes the genetic disease Aspartylglucosaminuria
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 298 | 0.2M Ammonium Acetate, 0.1M Bis-Tris pH 5.5, 25% Polyethylene glycol 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.94 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.04 | α = 81.51 |
b = 52.77 | β = 90.15 |
c = 61.89 | γ = 105.93 |
Symmetry | |
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Space Group | P 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 | 100 | CCD | ADSC QUANTUM 315r | 2012-04-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 0.9 | NSLS | X29A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.83 | 50.15 | 92.6 | 18.8 | 3.8 | 45208 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.83 | 1.87 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1P4K | 1.83 | 20 | 42925 | 2265 | 92.56 | 0.1577 | 0.15568 | 0.19667 | RANDOM | 17.83 |
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] | |
-0.68 | 0.45 | -0.17 | 0.74 | -0.07 | -0.45 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.196 |
r_dihedral_angle_4_deg | 15.08 |
r_dihedral_angle_3_deg | 13.24 |
r_dihedral_angle_1_deg | 6.732 |
r_long_range_B_refined | 5.651 |
r_long_range_B_other | 5.507 |
r_scangle_other | 4.103 |
r_scbond_it | 2.672 |
r_scbond_other | 2.669 |
r_mcangle_other | 2.489 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4186 |
Nucleic Acid Atoms | |
Solvent Atoms | 332 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
iMOSFLM | data reduction |
Aimless | data scaling |
MOLREP | phasing |