1JAZ
Crystal Structure of Monoclinic Form of D90E Mutant of Escherichia coli Asparaginase II
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3ECA | MONOMER A FROM NATIVE L-ASPARAGINASE II STRUCTURE - PDB CODE: 3ECA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | PEG MME 550, MES, zinc sulfate, pH 6.5, 292 K, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 40.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.118 | α = 90 |
b = 133.076 | β = 108.78 |
c = 62.565 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | IMAGE PLATE | MARRESEARCH | Vertically focusing cylindrical pre-mirror | 1999-03-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I711 | 1.104 | MAX II | I711 |
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 | 2.27 | 25 | 98.6 | 0.098 | 28.9 | 4.9 | 26057 | 26057 | -3 | 36.4 |
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 | 2.27 | 2.35 | 87.3 | 0.143 | 6.2 | 2.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | 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 | MONOMER A FROM NATIVE L-ASPARAGINASE II STRUCTURE - PDB CODE: 3ECA | 2.27 | 10 | -3 | 24392 | 24392 | 1301 | 99.5 | 0.1828 | 0.1828 | 0.1802 | 0.232 | RANDOM | 22.56 |
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] | |
-0.71 | -1.44 | 0.73 | -0.95 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
p_planar_d | 4.396 |
p_scangle_it | 3.199 |
p_scbond_it | 2.062 |
p_angle_d | 1.639 |
p_mcangle_it | 1.199 |
p_mcbond_it | 0.672 |
p_chiral_restr | 0.1 |
p_bond_d | 0.016 |
p_plane_restr | 0.005 |
p_angle_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4587 |
Nucleic Acid Atoms | |
Solvent Atoms | 136 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
EPMR | phasing |
REFMAC | refinement |