2X1L
Crystal structure of Mycobacterium smegmatis methionyl-tRNA synthetase in complex with methionine and adenosine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1A8H | PDB ENTRY 1A8H |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 1.2 M NAH2PO4, 800 MM K2HPO4, 200 MM LI2SO4, 100 MM CAPS, PH 7.0, VAPOR DIFFUSION, HANGING DROPS, TEMPERATURE 293 K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.2 | 61 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 155.95 | ¦Á = 90 |
b = 138.91 | ¦Â = 124.84 |
c = 123.31 | ¦Ã = 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 | MULTILAYER MIRROR | 2008-10-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I911-2 | MAX II | I911-2 |
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 | 2.3 | 30 | 97.8 | 0.09 | 11.8 | 4.1 | 93306 | 2 | 39.6 |
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 | 2.3 | 2.42 | 96.1 | 0.38 | 3.2 | 3.8 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1A8H | 2.3 | 30 | 88634 | 4670 | 97.7 | 0.219 | 0.218 | 0.249 | RANDOM | 23.9 |
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] | |
1.43 | -0.39 | -0.82 | -1.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.638 |
r_dihedral_angle_4_deg | 12.955 |
r_dihedral_angle_3_deg | 12.422 |
r_dihedral_angle_1_deg | 4.134 |
r_angle_refined_deg | 0.886 |
r_scangle_it | 0.719 |
r_mcangle_it | 0.416 |
r_scbond_it | 0.398 |
r_mcbond_it | 0.223 |
r_symmetry_vdw_refined | 0.096 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11638 |
Nucleic Acid Atoms | |
Solvent Atoms | 484 |
Heterogen Atoms | 141 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |