5V0Q
Original engineered variant of I-OnuI meganuclease targeting the HIV integrase gene; harbors 49 point mutations relative to wild-type I-OnuI
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3QQY |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | 19% (w/v) PEG 2000, 6% (w/v) PEG-MME 8000, 100mM BIS-TRIS pH 8.0 200mM sodium chloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.42 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 39.693 | α = 90 |
b = 74.419 | β = 90 |
c = 164.861 | 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 | 108 | PIXEL | DECTRIS PILATUS3 S 6M | 2016-03-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 1.000 | ALS | 5.0.2 |
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 | 2.4 | 50 | 99.9 | 0.101 | 0.106 | 0.03 | 7.7 | 12.2 | 19980 | 45.63 |
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 | 2.4 | 2.49 | 99.6 | 0.8 | 0.835 | 0.237 | 0.893 | 11.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3QQY | 2.4 | 44.207 | 1.35 | 19890 | 1993 | 99.43 | 0.1901 | 0.1856 | 0.2298 | 48.5382 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 22.189 |
f_angle_d | 0.632 |
f_chiral_restr | 0.027 |
f_bond_d | 0.003 |
f_plane_restr | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2374 |
Nucleic Acid Atoms | 1066 |
Solvent Atoms | 63 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data reduction |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data scaling |
PHASER | phasing |
HKL | data scaling |