2HBJ
Structure of the yeast nuclear exosome component, Rrp6p, reveals an interplay between the active site and the HRDC domain
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 277 | 12-14% PEG 20000, 0.1M Mes or Hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.94 | 58.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 110.135 | α = 90 |
b = 110.135 | β = 90 |
c = 80.169 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 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 | MARRESEARCH | Si mirrors | 2005-06-10 | M | MAD | |||||
2 | 1 | x-ray | 100 | CCD | MARRESEARCH | Si mirrors | 2005-06-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7A | 0.8793, 1.072, 1.071, 1.5218 | EMBL/DESY, HAMBURG | BW7A |
2 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X13 | 0.8048 | EMBL/DESY, HAMBURG | X13 |
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 | ||||||||
1,2 | 2.1 | 55.06 | 98.5 | 0.058 | 12.7 | 4.9 | 33892 | 33892 | 40.822 |
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) | |||||||||||
2.1 | 2.18 | 91.3 | 91.3 | 0.503 | 2.6 | 3.6 | 3087 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 2.1 | 55.06 | 30976 | 30976 | 3087 | 93.6 | 0.239 | 0.239 | 0.232 | 0.292 | RANDOM | 54.97 |
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] | |
3.075 | 1.755 | 3.075 | -6.151 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.24403 |
c_angle_deg | 1.34773 |
c_improper_angle_d | 0.91265 |
c_bond_d | 0.008005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3216 |
Nucleic Acid Atoms | |
Solvent Atoms | 201 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
SHARP | phasing |
SOLOMON | phasing |
CNS | refinement |
PDB_EXTRACT | data extraction |
MAR345 | data collection |