1P9P
The Crystal Structure of a M1G37 tRNA Methyltransferase, TrmD
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 283 | MPD, acetate buffer at pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.92 | 57.87 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 97.255 | α = 90 |
b = 97.255 | β = 90 |
c = 62.661 | γ = 120 |
Symmetry | |
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Space Group | P 32 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 | 150 | CCD | 2002-06-15 | M | SINGLE WAVELENGTH | |||||||
2 | 1 | x-ray | 150 | CCD | 2002-09-15 | M | MAD | |||||||
1,2 | 1 |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.000 | APS | 17-ID |
2 | SYNCHROTRON | APS BEAMLINE 17-ID | 0.97920, 0.97031, 0.95373 | APS | 17-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | ||||||||
1,2 | 2.5 | 50 | 98.9 | 0.096 | 8.6 | 12013 | 51.1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
1,2 | 2.5 | 2.59 | 0.966 | 0.373 | 3.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MAD | 2.5 | 50 | 12013 | 11974 | 602 | 99.68 | 0.196 | 0.247 | random |
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 |
x_angle_d | 2.8 |
x_bond_d | 0.035 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1845 |
Nucleic Acid Atoms | |
Solvent Atoms | 43 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SCALEPACK | data scaling |
SOLVE | phasing |
CNX | refinement |
HKL-2000 | data reduction |