5IRA
Expanding Nature's Catalytic Repertoire -Directed Evolution of an Artificial Metalloenzyme for In Vivo Metathesis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2QCB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 293 | 1.5 M AmSO4, 0.1 M Na acetate, pH4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.496 | α = 90 |
b = 57.496 | β = 90 |
c = 183.415 | γ = 90 |
Symmetry | |
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Space Group | I 41 2 2 |
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 16M | 2016-02-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 0.999989 | SLS | X06SA |
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 | 1.5 | 45.85 | 100 | 0.066 | 26.4 | 21.2 | 25264 |
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 | 1.5 | 1.53 | 100 | 1.228 | 2.6 | 19.1 |
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 | 2QCB | 1.5 | 45.85 | 23966 | 1269 | 100 | 0.137 | 0.135 | 0.174 | RANDOM | 25.34 |
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] | |
-0.57 | -0.57 | 1.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.049 |
r_sphericity_free | 25.014 |
r_sphericity_bonded | 14.153 |
r_dihedral_angle_4_deg | 12.973 |
r_dihedral_angle_3_deg | 12.642 |
r_dihedral_angle_1_deg | 7.829 |
r_long_range_B_refined | 6.261 |
r_rigid_bond_restr | 5.683 |
r_scbond_it | 5.646 |
r_long_range_B_other | 5.193 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 913 |
Nucleic Acid Atoms | |
Solvent Atoms | 65 |
Heterogen Atoms | 42 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |