6OQ5
Structure of the full-length Clostridium difficile toxin B in complex with 3 VHHs
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2BVL | 2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2 |
experimental model | PDB | 4R04 | 2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2 |
experimental model | PDB | 3PEE | 2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2 |
experimental model | PDB | 6C0B | 2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2 |
experimental model | PDB | 3V0A | 2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2 |
experimental model | PDB | 4NP4 | 2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2 |
experimental model | PDB | 4NC2 | 2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 291 | 0.1 M sodium acetate, 0.1M magnesium acetate, and 5% PEG 8K (final pH 5.2) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.58 | 65.61 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 149.619 | ¦Á = 90 |
b = 168.565 | ¦Â = 90 |
c = 179.921 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2016-06-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.97918 | APS | 24-ID-C |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3.87 | 48.91 | 99.4 | 0.137 | 7.7 | 3.7 | 42971 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3.87 | 3.97 | 1.548 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2 | 3.87 | 48.91 | 40731 | 2203 | 99.22 | 0.26541 | 0.26275 | 0.31516 | RANDOM | 169.399 |
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] | |
-2.6 | 2.48 | 0.13 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.591 |
r_long_range_B_refined | 21.701 |
r_dihedral_angle_4_deg | 16.699 |
r_dihedral_angle_3_deg | 15.806 |
r_mcangle_it | 10.572 |
r_dihedral_angle_1_deg | 7.891 |
r_mcbond_it | 6.114 |
r_scbond_it | 5.715 |
r_angle_refined_deg | 1.097 |
r_chiral_restr | 0.093 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 21501 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 2 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |