6UKG
HhaI endonuclease in Complex With DNA in space group P21 (pH 4.2)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6UKE | PDB entry 6UKE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 292 | 10% v/v 2-propanol, sodium phosphate / citric acid, pH 4.2, 0.2 M lithium sulfate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.99 | 38.25 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.849 | α = 90 |
b = 37.545 | β = 110.256 |
c = 69.923 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | PIXEL | DECTRIS EIGER X 16M | 2018-12-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.00000 | APS | 22-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.16 | 31.52 | 88.9 | 0.093 | 0.039 | 14.5 | 6.1 | 192216 | 11.7 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.16 | 1.21 | 66.5 | 0.354 | 0.217 | 0.863 | 3.6 | 3.2 |
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 | THROUGHOUT | PDB entry 6UKE | 1.16 | 31.52 | 1.36 | 181702 | 3656 | 88.88 | 0.1412 | 0.1409 | 0.1572 | 20.21 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 22.8142 |
f_angle_d | 0.9956 |
f_chiral_restr | 0.0703 |
f_plane_restr | 0.0075 |
f_bond_d | 0.0073 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2089 |
Nucleic Acid Atoms | 894 |
Solvent Atoms | 270 |
Heterogen Atoms | 27 |
Software
Software | |
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Software Name | Purpose |
SERGUI | data collection |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHENIX | phasing |