4O0H
Crystal structure of human L-asparaginase protein with covalently linked substrate L-asparagine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4GDV | PDB entry 4GDV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 2.2-2.5 M sodium Malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.28 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 59.651 | ¦Á = 90 |
b = 59.651 | ¦Â = 90 |
c = 298.517 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 65 |
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 | 93 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2012-05-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.97 | 30 | 91.9 | 0.097 | 9.16 | 3.36 | 38615 | 38615 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.97 | 2.09 | 80.5 | 0.435 | 2.05 | 3.07 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 4GDV | 1.97 | 29.83 | 35707 | 35716 | 1794 | 89.37 | 0.16881 | 0.16565 | 0.23139 | RANDOM | 26.228 |
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] | |
-7.9 | -7.9 | 15.81 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.503 |
r_dihedral_angle_3_deg | 18.5 |
r_dihedral_angle_4_deg | 17.275 |
r_dihedral_angle_1_deg | 7.951 |
r_long_range_B_refined | 3.34 |
r_long_range_B_other | 3.291 |
r_mcangle_other | 2.076 |
r_mcangle_it | 2.048 |
r_scangle_other | 2.005 |
r_angle_refined_deg | 1.655 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4294 |
Nucleic Acid Atoms | |
Solvent Atoms | 193 |
Heterogen Atoms | 18 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
MOLREP | phasing |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |