7LOV
Crystal structure of Clostridium difficile Toxin B (TcdB) glucosyltransferase in complex with UDP and noeuromycin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5UQM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 295 | 85 mM Sodium Citrate pH 5.6, 170 mM Ammonium Acetate, 25.5 % (w/v) PEG 4000, 15 %(v/v) Glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 55.66 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 152.589 | α = 90 |
b = 82.676 | β = 92.43 |
c = 113.227 | 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 | PIXEL | DECTRIS EIGER X 9M | 2020-01-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 17-ID-1 | 0.9790 | NSLS-II | 17-ID-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 2.5 | 28.97 | 99.9 | 0.27 | 0.99 | 6.2 | 7 | 48863 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.5 | 2.58 | 99.9 | 1.79 | 0.5 | 1.3 | 7.1 |
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 | 5UQM | 2.5 | 28.97 | 46524 | 2334 | 99.9 | 0.21 | 0.2081 | 0.2478 | RANDOM | 39.964 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
2.5 | -0.21 | -1.21 | -1.27 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.275 |
r_dihedral_angle_4_deg | 16.53 |
r_dihedral_angle_3_deg | 15.513 |
r_dihedral_angle_1_deg | 5.779 |
r_angle_refined_deg | 1.219 |
r_angle_other_deg | 1.125 |
r_chiral_restr | 0.044 |
r_bond_refined_d | 0.003 |
r_gen_planes_refined | 0.003 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8808 |
Nucleic Acid Atoms | |
Solvent Atoms | 223 |
Heterogen Atoms | 104 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |