5CD1
Structure of an asymmetric tetramer of human tRNA m1A58 methyltransferase in a complex with SAH and tRNA3Lys
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 289 | 1 microliter protein solution (4.8 mg/ml protein, 66.4 micromolar tRNA3Lys, 2mM SAH, 1mM MgCl2 and 50mM Hepes pH7.5) mixed with 1 microliter reservoir solution (0.1M NaAcetate, pH4.8-5.0,2% w/v PEG 4000, and 15% v/v MPD) over 1000 microliter reservoir solution |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.1 | 60.29 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 128.24 | α = 90 |
b = 137.44 | β = 90 |
c = 157.59 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 103.15 | CCD | ADSC QUANTUM 315r | 2014-09-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.11587 | ALS | 8.3.1 |
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 | 3.6 | 102.3 | 99.3 | 0.308 | 6.4 | 4.3 | 32882 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 3.6 | 3.69 | 99.8 | 1.87 | 1 | 4.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation 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 | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 5CCB | 3.6 | 59.392 | 1.33 | 32711 | 1636 | 99.3 | 0.2337 | 0.2316 | 0.2729 | Random selection |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.049 |
f_angle_d | 0.763 |
f_chiral_restr | 0.04 |
f_bond_d | 0.004 |
f_plane_restr | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9637 |
Nucleic Acid Atoms | 3200 |
Solvent Atoms | |
Heterogen Atoms | 54 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |