3UGO
Crystal structure of RNA-polymerase sigma subunit domain 2 complexed with -10 promoter element ssDNA oligo (TACAAT)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1KU2 | PDB ENTRY 1KU2 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 295 | 5% PEG8000, 20% PEG300, 10% glycerol, 0.15% mellitic acid, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.97 | 58.61 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 86.134 | α = 90 |
b = 86.134 | β = 90 |
c = 111.728 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 4 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 77 | CCD | ADSC QUANTUM 315r | 2009-07-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 1.08090 | NSLS | X29A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.096 | 25 | 99.9 | 0.094 | 0.094 | 33.55 | 8.2 | 25331 | 25306 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.096 | 2.18 | 99.9 | 0.712 | 0.712 | 4.04 | 8.1 | 2471 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 1KU2 | 2.096 | 24.483 | 1.33 | 25306 | 1318 | 99.79 | 0.1982 | 0.1961 | 0.2366 |
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] | |
-11.4827 | -11.4827 | 23.1439 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 19.478 |
f_angle_d | 1.121 |
f_chiral_restr | 0.056 |
f_bond_d | 0.008 |
f_plane_restr | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1456 |
Nucleic Acid Atoms | 313 |
Solvent Atoms | 131 |
Heterogen Atoms | 5 |
Software
Software | |
---|---|
Software Name | Purpose |
CBASS | data collection |
PHASER | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |