3K1F
Crystal structure of RNA Polymerase II in complex with TFIIB
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3HOU | First 12-subunit RNA Polymerase II from PDB entry 3HOU |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 800 mM sodium ammonium tartrate, 100 mM HEPES pH 7.5, 5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.82 | 78.88 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 220.97 | α = 90 |
b = 408.27 | β = 90 |
c = 275.24 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | CCD | ADSC QUANTUM 4 | silicon crystal monochromator | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.9340 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 4.3 | 40 | 99.3 | 0.13 | 11.5 | 4.7 | 83919 | 83919 | -3 | 57.5 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 4.3 | 4.3 | 98.2 | 0.99 | 2 | 4.7 | 6050 |
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 | First 12-subunit RNA Polymerase II from PDB entry 3HOU | 4.3 | 39.69 | 83918 | 83918 | 2058 | 99.4 | 0.221 | 0.221 | 0.22 | 0.255 | RANDOM | 124.4 |
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] | |
16.7149 | 25.3097 | -42.0246 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
o_angle_deg | 1.16 |
o_bond_d | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 32323 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 9 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
PHASER | phasing |
BUSTER | refinement |
XDS | data reduction |
XSCALE | data scaling |