2V7R
Crystal structure of a human tRNAGly microhelix at 1.2 Angstrom resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 40 MM SODIUM CACODYLATE, PH 6.0, 12 MM SPERMINE TETRA-HCL, 12 MM SODIUM CHLORIDE, 80 MM POTASSIUM CHLORIDE, 10% (V/V) MPD, EQUILIBRATED AGAINST 35% (V/V) MPD AT ROOM TEMPERATURE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 59.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 37.12 | α = 90 |
b = 37.491 | β = 113.02 |
c = 30.379 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | CCD | MARRESEARCH | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X13 | EMBL/DESY, HAMBURG | X13 |
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 | 1.2 | 50 | 95.3 | 0.05 | 18.1 | 7.2 | 11547 | 2 |
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 | 1.2 | 1.22 | 93.7 | 0.24 | 7.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.2 | 14.08 | 10934 | 568 | 95.4 | 0.188 | 0.187 | 0.208 | RANDOM | 14.82 |
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] | |
-0.01 | -0.05 | -0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scangle_it | 2.604 |
r_scbond_it | 2.395 |
r_angle_refined_deg | 1.712 |
r_nbtor_refined | 0.274 |
r_nbd_refined | 0.165 |
r_symmetry_hbond_refined | 0.146 |
r_xyhbond_nbd_refined | 0.121 |
r_symmetry_vdw_refined | 0.113 |
r_chiral_restr | 0.062 |
r_gen_planes_refined | 0.014 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 293 |
Solvent Atoms | 85 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |