3U1U
Crystal structure of RNA polymerase-associated protein RTF1 homolog Plus-3 domain
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | sitting drop vapor diffusion | 5.5 | 291 | 25% PEG-3350, 0.2M ammonium sulfate, 0.1M sodium cacodylate, pH 5.5, sitting drop vapor diffusion, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 53.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 47.479 | α = 90 |
b = 50.369 | β = 103.37 |
c = 69.776 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
xds | 1 | 100 | ||||||||||||
1 | 1 | x-ray | IMAGE PLATE | RIGAKU RAXIS | 2011-08-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | Rigaku FR-E | 1.5418 |
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 | 1.8 | 30 | 99.86 | 0.076 | 18.0335 | 7.2 | 29993 | 29882 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
1 | 1.8 | 1.9 | 99.51 | 0.89 | 7.07 | 4298 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.8 | 28.54 | 29923 | 29857 | 1513 | 99.78 | 0.2036 | 0.2018 | 0.2349 | THIN SHELLS (SFTOOLS) | 27.0878 |
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] | |
0.78 | -0.6 | 0.27 | -1.33 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.349 |
r_dihedral_angle_4_deg | 18.832 |
r_dihedral_angle_3_deg | 12.591 |
r_dihedral_angle_1_deg | 6.132 |
r_scangle_it | 3.398 |
r_scbond_it | 2.146 |
r_angle_refined_deg | 1.355 |
r_mcangle_it | 1.193 |
r_angle_other_deg | 0.881 |
r_mcbond_it | 0.683 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2071 |
Nucleic Acid Atoms | |
Solvent Atoms | 103 |
Heterogen Atoms | 49 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
SHELX | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
JDirector | data collection |
XDS | data reduction |
ARP/wARP | model building |
Coot | model building |