4V7J
Structure of RelE nuclease bound to the 70S ribosome (precleavage state)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2WH1 | PDB ENTRY 2WH1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.2 | 293 | 0.1M Tris-HAc, 0.2M KSCN, 3-4.5% w/v PEG 20k, 3-4.5% PEG 550 monomethylether, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.3 | 62.75 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 211.571 | α = 90 |
b = 451.963 | β = 90 |
c = 622.438 | 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 | 100 | PIXEL | PSI PILATUS 6M | 2009-06-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.000 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 3.3 | 50 | 99.8 | 0.0163 | 0.0163 | 9.8 | 8.46 | 885437 | 883810 | -3 | -3 | 76.1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3.3 | 3.4 | 99.6 | 0.0119 | 0.0119 | 1.95 | 7.43 | 75083 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2WH1 | 3.3 | 50 | 885437 | 883807 | 40918 | 99.8 | 0.219 | 0.219 | 0.219 | 0.247 | RANDOM | 116.4 |
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] | |
-5.38 | 1.33 | 4.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_angle_deg | 1.17 |
c_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 19866 |
Nucleic Acid Atoms | 35872 |
Solvent Atoms | |
Heterogen Atoms | 237 |
Software
Software | |
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Software Name | Purpose |
IDL | data collection |
CNS | refinement |
XDS | data reduction |
XDS | data scaling |
CNS | phasing |