6V2C
Complex of mutant (K162M) of E. coli L-asparaginase II with L-Asp. Covalent acyl-enzyme intermediate and tetrahedral intermediate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3ECA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 293 | 0.1 M sodium acetate, pH 5, 5 mM L-Asp, and 18-20% (w/v) PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 41.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.698 | α = 90 |
b = 125.914 | β = 90 |
c = 130.108 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | PIXEL | DECTRIS EIGER X 4M | Multilayer X-ray mirrors VariMax HF | 2019-03-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 40 | 97.3 | 0.074 | 0.081 | 0.033 | 12.3 | 5.3 | 79835 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2 | 2.03 | 94 | 0.73 | 0.852 | 0.427 | 0.615 | 3.3 |
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 | 3eca | 2 | 27.69 | 76301 | 2405 | 95.7 | 0.173 | 0.171 | 0.235 | RANDOM | 28.75 |
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] | |
-3.48 | 1.68 | 1.79 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.029 |
r_dihedral_angle_1_deg | 18.096 |
r_dihedral_angle_4_deg | 16.524 |
r_dihedral_angle_3_deg | 15.798 |
r_angle_refined_deg | 2.234 |
r_angle_other_deg | 2.064 |
r_chiral_restr | 0.113 |
r_bond_refined_d | 0.019 |
r_gen_planes_refined | 0.013 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9814 |
Nucleic Acid Atoms | |
Solvent Atoms | 949 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
PHASER | phasing |