5EPE
Crystal structure of SAM-dependent methyltransferase from Thiobacillus denitrificans in complex with S-Adenosyl-L-homocysteine
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 9.5 | 289 | 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG II condition #56 (0.1M CHES pH=9.5, 20%w/v PEG 4K) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 1 mg/ml TEV solution at 289 K for 3 hours |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.97 | 58.55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 157.536 | α = 90 |
b = 157.536 | β = 90 |
c = 157.536 | γ = 90 |
Symmetry | |
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Space Group | F 2 3 |
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 300 mm CCD | Beryllium Lenses | 2015-04-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.9 | 50 | 100 | 0.1 | 0.1 | 0.105 | 0.031 | 5.6 | 11.4 | 25623 | 25623 | -3 | 25.4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.9 | 1.93 | 100 | 0.914 | 0.96 | 0.292 | 0.81 | 2 | 10.7 | 1254 |
Refinement
Statistics | |||||||||||||||||||
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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 | SAD | THROUGHOUT | 1.9 | 50 | 24340 | 1266 | 99.97 | 0.1371 | 0.1356 | 0.1671 | RANDOM | 32.68 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.679 |
r_dihedral_angle_4_deg | 19.522 |
r_dihedral_angle_3_deg | 12.367 |
r_dihedral_angle_1_deg | 6.349 |
r_mcangle_it | 1.767 |
r_angle_refined_deg | 1.717 |
r_mcbond_it | 1.106 |
r_mcbond_other | 1.095 |
r_angle_other_deg | 0.987 |
r_chiral_restr | 0.106 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1893 |
Nucleic Acid Atoms | |
Solvent Atoms | 276 |
Heterogen Atoms | 27 |
Software
Software | |
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Software Name | Purpose |
BLU-MAX | data collection |
HKL-3000 | data scaling |
HKL-3000 | phasing |
SHELX | phasing |
DM | phasing |
MLPHARE | phasing |
REFMAC | refinement |
Coot | model building |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |