6UGG
Structure of unmodified E. coli tRNA(Asp)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1EHZ | PDB entry 1EHZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 287 | 2 uL 20 mg/ml E. coli tRNA(Asp) + 2 uL equilibration solution (50 mM sodium cacodylate, pH 7.5, 30% MPD, 10 mM spermine tetrahydrochloride, 300 mM sodium chloride, 300 mM potassium chloride) + 0.5 uL 0.25% w/v p-coumaric acid, 0.25% w/v phenylurea, 0.25% w/v poly(3-hydroxybutyric acid), 0.25% w/v sulfaguanidine, 0.02 M sodium HEPES, pH 6.8 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.677 | α = 90 |
b = 64.677 | β = 90 |
c = 195.799 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 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 EIGER X 9M | Monochromator | 2017-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.0782 | APS | 21-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 1.95 | 48.62 | 94 | 0.155 | 0.158 | 0.029 | 0.992 | 15.8 | 30 | 35638 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.95 | 2.056 | 50.8 | 2.683 | 2.724 | 0.468 | 0.488 | 1.8 | 33.7 |
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 | PDB entry 1EHZ | 1.95 | 48.62 | 30070 | 1469 | 88.5 | 0.2164 | 0.2154 | 0.2381 | RANDOM | 50.999 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
2.3 | 2.3 | -4.59 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_angle_other_deg | 1.298 |
r_angle_refined_deg | 0.85 |
r_chiral_restr | 0.07 |
r_gen_planes_refined | 0.005 |
r_bond_refined_d | 0.003 |
r_bond_other_d | 0.002 |
r_gen_planes_other | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 3288 |
Solvent Atoms | 23 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
STARANISO | data scaling |
PHASER | phasing |