8AJY
Ruminococcus flavefaciens Cohesin-Dockerin structure: dockerin from ScaH adaptor scaffoldin in complex with the cohesin from ScaE anchoring scaffoldin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4IU2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2 M Lithium sulfate monohydrate, 0.1 M TRIS hydrochloride pH 8.5 and 30% w/v Polyethylene glycol 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.37 | 48.01 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.81 | α = 90 |
b = 120 | β = 97.77 |
c = 65.95 | γ = 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 | PIXEL | DECTRIS PILATUS 2M | 2018-03-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.873127 | ESRF | ID23-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.71 | 65.344 | 99.6 | 0.108 | 0.124 | 0.061 | 0.994 | 8 | 3.8 | 66981 |
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 | 1.714 | 1.743 | 99.3 | 0.5 | 0.59 | 0.308 | 0.789 | 2.1 | 3.4 |
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 | 4IU2 | 1.71 | 65.34 | 63640 | 3334 | 99.55 | 0.1961 | 0.1939 | 0.2372 | RANDOM | 18.864 |
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] | |
-0.9 | -0.23 | 1.43 | -0.45 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.114 |
r_dihedral_angle_3_deg | 12.491 |
r_dihedral_angle_4_deg | 12.266 |
r_dihedral_angle_1_deg | 7.091 |
r_angle_refined_deg | 1.878 |
r_angle_other_deg | 1.524 |
r_chiral_restr | 0.088 |
r_bond_refined_d | 0.015 |
r_gen_planes_refined | 0.012 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4296 |
Nucleic Acid Atoms | |
Solvent Atoms | 428 |
Heterogen Atoms | 83 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
autoPROC | data reduction |
autoPROC | data scaling |
PHASER | phasing |