5KNN
Evolutionary gain of alanine mischarging to non-cognate tRNAs with a G4:U69 base pair
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3HXU |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 289 | 0.1 M Hepes pH 7.5, 20% Polyethylene glycol 3350, 0.2 M MgCl2 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.55 | 51.74 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 52.167 | α = 90.07 |
b = 98.26 | β = 89.95 |
c = 201.385 | γ = 90.11 |
Symmetry | |
---|---|
Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2012-11-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 1.1271 | SSRL | BL11-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.68 | 50 | 99.2 | 0.142 | 5.5 | 6.9 | 100341 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.68 | 2.73 | 88.7 | 0.408 | 0.894 | 6.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3HXU | 2.68 | 49.13 | 100341 | 5119 | 93.42 | 0.2179 | 0.216 | 0.2542 | RANDOM | 55.755 |
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] | |
-10.09 | 5.36 | -19.53 | -1.42 | -27.27 | 11.52 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.608 |
r_dihedral_angle_4_deg | 18.377 |
r_dihedral_angle_3_deg | 17.603 |
r_mcangle_it | 6.913 |
r_dihedral_angle_1_deg | 6.595 |
r_mcbond_it | 4.478 |
r_mcbond_other | 4.478 |
r_angle_other_deg | 3.151 |
r_angle_refined_deg | 1.996 |
r_chiral_restr | 0.122 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 28360 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 224 |
Software
Software | |
---|---|
Software Name | Purpose |
HKL-2000 | data collection |
HKL-2000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |