5AWH
Rhodobacter sphaeroides Argonaute in complex with guide RNA/target DNA heteroduplex
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 0.05 M sodium cacodylate trihydrlate (pH 7.0), 42% (v/v) 2-methyl-2,4-pentanediol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.46 | 50.09 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.186 | α = 90 |
b = 118.303 | β = 95.83 |
c = 118.48 | 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 | CCD | ADSC QUANTUM 210r | 2014-06-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NW12A | 0.97921 | Photon Factory | AR-NW12A |
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 | 50 | 97.7 | 0.063 | 0.074 | 0.039 | 15.3 | 3.8 | 123866 |
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 | 2 | 2.03 | 100 | 0.4 | 3.8 |
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 | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 2 | 35.63 | 117604 | 6232 | 97.08 | 0.1866 | 0.1842 | 0.2325 | RANDOM | 58.291 |
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] | |
-2.68 | 0.12 | 3.85 | -1.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.477 |
r_dihedral_angle_4_deg | 19.568 |
r_dihedral_angle_3_deg | 16.51 |
r_dihedral_angle_1_deg | 6.827 |
r_mcangle_it | 3.931 |
r_mcbond_it | 2.87 |
r_mcbond_other | 2.87 |
r_angle_refined_deg | 1.758 |
r_angle_other_deg | 0.968 |
r_chiral_restr | 0.11 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11669 |
Nucleic Acid Atoms | 1498 |
Solvent Atoms | 636 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SHARP | phasing |
HKL-2000 | data reduction |