Crystal Structure of the Surface Protein (CD630_07380) from Clostridium difficile Strain 630
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 292 | Protein: 8.4 mg/ml, 0.25M Sodium chloride, 0.01M Tris buffer pH 8.3; Screen: JSCG+ (H8), 0.2M Sodim chloride, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350; Cryo: 0.2M Sodim chloride, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.84 | 33.3 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 42.08 | ¦Á = 90 |
b = 94.872 | ¦Â = 89.99 |
c = 57.093 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 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 | CCD | MARMOSAIC 300 mm CCD | 2018-02-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
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) | 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 | 1.85 | 30 | 100 | 0.107 | 0.107 | 0.122 | 0.059 | 1 | 13.1 | 4.3 | 37762 | -3 | 24.3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.85 | 1.88 | 100 | 0.988 | 0.988 | 0.548 | 0.656 | 1.9 | 4.2 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.85 | 28.55 | 35814 | 1924 | 99.08 | 0.18146 | 0.1792 | 0.1915 | 0.22399 | 0.2345 | RANDOM | 28.106 |
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] | |
-15.14 | -4.85 | 31.54 | -16.4 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_long_range_B_refined | 6.84 |
r_long_range_B_other | 6.833 |
r_dihedral_angle_3_deg | 5.472 |
r_scangle_other | 4.875 |
r_mcangle_it | 3.762 |
r_mcangle_other | 3.762 |
r_scbond_it | 3.208 |
r_scbond_other | 3.207 |
r_dihedral_angle_1_deg | 2.552 |
r_mcbond_it | 2.548 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4211 |
Nucleic Acid Atoms | |
Solvent Atoms | 184 |
Heterogen Atoms | 108 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHASER | phasing |