3BT7
Structure of E. coli 5-Methyluridine Methyltransferase TrmA in complex with 19 nucleotide T-arm analogue
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2BH2 | PDB entry 2BH2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.4 | 295 | 100 mM sodium cacodylate pH 7.4, 200 mM sodium sulfate, and 22 % PEG-8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.1 | 60.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 184.407 | α = 90 |
b = 70.131 | β = 120.88 |
c = 107.95 | 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 | ADSC QUANTUM 315r | 2007-01-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.11 | 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 | 2.43 | 35.1 | 0.078 | 5.7 | 2.2 | 90859 | 42023 | 2 | 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 | 2.43 | 2.49 | 83.7 | 0.27 | 1.7 | 2 |
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 | SAD | THROUGHOUT | PDB entry 2BH2 | 2.43 | 35.07 | 38764 | 3230 | 93.62 | 0.2297 | 0.22509 | 0.28635 | RANDOM | 47.563 |
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] | |
-0.02 | -0.01 | 0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.587 |
r_dihedral_angle_3_deg | 20.099 |
r_dihedral_angle_4_deg | 15.169 |
r_dihedral_angle_1_deg | 6.715 |
r_scangle_it | 3.392 |
r_scbond_it | 2.102 |
r_angle_refined_deg | 1.781 |
r_mcangle_it | 1.453 |
r_angle_other_deg | 1.434 |
r_mcbond_it | 0.78 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5914 |
Nucleic Acid Atoms | 804 |
Solvent Atoms | 261 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SOLVE | phasing |
DM | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
SCALA | data scaling |