5XZ1
Crystal structure of the Homo Sapiens cytoplasmic ribosomal decoding site in complex with G418
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 2-methyl-2,4-pentandiol, Sodium cacodylate, Spermine tetrahydrochloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.63 | 53.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 47.399 | α = 90 |
b = 32.528 | β = 95.58 |
c = 96.484 | 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 | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 2M-F | 2015-06-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-1A | 1.1 | Photon Factory | BL-1A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | 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 | 3.01 | 48.013 | 98.5 | 0.07 | 0.084 | 0.998 | 12.46 | 3.285 | 5988 | -3 | 54.56 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 3.01 | 3.09 | 95.8 | 0.356 | 0.428 | 0.921 | 2.53 | 3.005 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3.008 | 48.013 | 1.35 | 5949 | 568 | 97.86 | 0.193 | 0.199 | 59.13 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.7 |
f_angle_d | 1.348 |
f_chiral_restr | 0.667 |
f_plane_restr | 0.02 |
f_bond_d | 0.018 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 1864 |
Solvent Atoms | 25 |
Heterogen Atoms | 136 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |