3KFL
Leishmania major methionyl-tRNA synthetase in complex with methionyladenylate and pyrophosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2CSX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 298 | 2 microliters 24.44 mg/ml protein soln. [in 25 mM HEPES (pH 7.0), 500 mM NaCl, 0.025% Na-azide, 5% glycerol, 0.01 mM ZnCl2, 10 mM L-Met, 10 mM ATP] + 2 microliters well soln. [0.2 M K-formate, 26% PEG 3350 and additives of 10 mM L-Met and 1 mM TCEP]; crystal cryoprotected by quick soak in mother liquor supplemented with 15% ethylene glycol, vapor diffusion, hanging drop, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 49.39 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.816 | α = 90 |
b = 88.802 | β = 90 |
c = 101.779 | 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 | CCD | MARMOSAIC 325 mm CCD | 2009-04-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.97923 | SSRL | BL9-2 |
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 | 50 | 100 | 0.079 | 8.6 | 5.3 | 42546 | 5 | 27.6 |
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) | |||||||||||
2 | 2.07 | 100 | 0.699 | 1.8 | 5.4 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2csx | 2 | 37.16 | 42461 | 2141 | 99.7 | 0.17 | 0.17033 | 0.16826 | 0.20871 | RANDOM | 38.029 |
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] | |
-1.2 | 4.18 | -2.98 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.248 |
r_dihedral_angle_3_deg | 13.446 |
r_dihedral_angle_4_deg | 11.738 |
r_dihedral_angle_1_deg | 5.815 |
r_scangle_it | 4.297 |
r_scbond_it | 3.141 |
r_mcangle_it | 2.397 |
r_mcbond_it | 1.66 |
r_angle_refined_deg | 1.197 |
r_angle_other_deg | 0.849 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4240 |
Nucleic Acid Atoms | |
Solvent Atoms | 217 |
Heterogen Atoms | 82 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Blu-Ice | data collection |
HKL-2000 | data reduction |
BALBES | phasing |