3K7A
Crystal Structure of an RNA polymerase II-TFIIB complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1R5U | 1R5U WITHOUT CHAIN M |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.9 | 295 | 1.2 M sodium/potassium phosphate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.57 | 73.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 204.15 | α = 90 |
b = 216.21 | β = 90 |
c = 420.98 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 2 |
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 | 93 | CCD | MARMOSAIC 325 mm CCD | 2008-08-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.97946 | SSRL | BL12-2 |
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 | 3.8 | 210.49 | 98.6 | 0.093 | 0.093 | 9.6 | 3.9 | 89990 |
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) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 3.8 | 4.01 | 99.3 | 0.545 | 0.545 | 0.75 | 0.37 | 1.3 | 3.9 | 13147 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1R5U WITHOUT CHAIN M | 3.8 | 50 | 87509 | 4320 | 95.51 | 0.268 | 0.263 | 0.313 | RANDOM | 188.144 |
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] | |
57.328 | -22.441 | -34.888 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_mcangle_it | 49.942 |
r_dihedral_angle_2_deg | 42.006 |
r_mcbond_it | 36.389 |
r_scangle_it | 30.115 |
r_scbond_it | 22.238 |
r_dihedral_angle_3_deg | 17.839 |
r_dihedral_angle_4_deg | 17.78 |
r_dihedral_angle_1_deg | 5.222 |
r_angle_refined_deg | 1.363 |
r_chiral_restr | 0.09 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 29020 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 9 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CNS | refinement |