5BP9
Crystal structure of SAM-dependent methyltransferase from Bacteroides fragilis 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 | 6.5 | 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 TOP96 condition #29 (0.2 M Ammonium sulfate, 0.1 M Sodium Cacodylate:HCl pH 6.5, 30% (w/v) PEG 8000) 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 |
1.95 | 31.55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.732 | α = 90 |
b = 70.66 | β = 90 |
c = 78.743 | 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 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 | 1.5 | 50 | 98.9 | 0.062 | 0.062 | 0.069 | 0.03 | 11.3 | 5 | 38281 | 37846 | -3 | 18.8 |
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 | 1.5 | 1.53 | 98 | 0.692 | 0.784 | 0.362 | 0.677 | 1.9 | 4.4 | 1807 |
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 | 1.5 | 50 | 35821 | 1836 | 98.93 | 0.1341 | 0.1318 | 0.1795 | RANDOM | 22.973 |
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] | |
0.13 | 0.4 | -0.53 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.027 |
r_sphericity_bonded | 16.133 |
r_dihedral_angle_4_deg | 11.605 |
r_dihedral_angle_3_deg | 11.552 |
r_rigid_bond_restr | 7.225 |
r_dihedral_angle_1_deg | 5.562 |
r_mcangle_it | 3.277 |
r_mcbond_it | 3.105 |
r_mcbond_other | 3.053 |
r_angle_refined_deg | 1.562 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1853 |
Nucleic Acid Atoms | |
Solvent Atoms | 338 |
Heterogen Atoms | 53 |
Software
Software | |
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Software Name | Purpose |
BLU-MAX | data collection |
HKL-3000 | data reduction |
HKL-3000 | phasing |
HKL-3000 | data scaling |
SHELX | phasing |
MLPHARE | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |