5L0Z
Crystal Structure of AdoMet bound rRNA methyltransferase from Sinorhizobium meliloti
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 300 | 5mM Cobalt chloride , 5mM Magnesium chloride hexahydrate, 0.1M HEPES pH 7.5, 9% wt/vol polyethylene glycol 3,350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 46.98 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.855 | α = 90 |
b = 82.896 | β = 90 |
c = 108.806 | 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 | 100 | IMAGE PLATE | RIGAKU RAXIS IV | 2015-08-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.542 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.9 | 65.94 | 100 | 0.86 | 28.51 | 6.7 | 13571 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.9 | 65.94 | 12403 | 634 | 96.23 | 0.19437 | 0.19087 | 0.26498 | RANDOM | 56.424 |
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] | |
0.54 | -0.89 | 0.34 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.897 |
r_dihedral_angle_4_deg | 19.716 |
r_dihedral_angle_3_deg | 18.907 |
r_dihedral_angle_1_deg | 7.549 |
r_long_range_B_refined | 5.616 |
r_long_range_B_other | 5.615 |
r_scangle_other | 3.491 |
r_mcangle_it | 3.404 |
r_mcangle_other | 3.404 |
r_scbond_it | 2.086 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3951 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 68 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data processing |
HKL-3000 | data scaling |
REFMAC | refinement |