6NJY
Type IV CRISPR associated RNA endonuclease Cas6 - apo form
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5 | 293 | Mother Liquor = 0.1 M sodium acetate trihydrate (pH 5.0) and 1.75M ammonium sulfate. 6-8 mg/ml of protein purified in 100 mM HEPES pH 7.5, 150 mM KCl, 5% glycerol, 1mM TCEP, was mixed in equal volumes (2 microliters of each) on a sitting drop pedestal with ~500 mL of mother liquor in reservoir. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.66 | 53.81 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 85.541 | α = 90 |
b = 85.541 | β = 90 |
c = 142.587 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 | 193 | PIXEL | DECTRIS PILATUS 6M | 2018-02-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 1.55, 1.0718 | SSRL | BL12-2 |
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 | 1.76 | 40.004 | 99.6 | 0.053 | 0.058 | 0.023 | 18.1 | 6 | 58149 | 33.22 |
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 | 1.76 | 1.82 | 96.3 | 0.727 | 0.822 | 0.376 | 0.736 | 4.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.76 | 40.004 | 56932 | 1966 | 97.55 | 0.1682 | 0.1672 | 0.1978 | 50.4429 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3721 |
Nucleic Acid Atoms | |
Solvent Atoms | 155 |
Heterogen Atoms | 191 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data scaling |
SOLVE | phasing |
RESOLVE | model building |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |