6TRH
Structure of E70A mutant of Rex8A from Paenibacillus barcinonensis complexed with 3(3)-alpha-L-arabinofuranosyl-xylotetraose.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6SRD |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 291 | 20% PEG 3350, 0.2M Potassium thiocyanate, 0.1M Bis Tris propane pH 7.5. Microseeding. Co-crystallization: 5 mM 3(3)-alpha-L-arabinofuranosyl-xylotetraose. Cryoprotectant: 25% Glycerol. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 82.295 | α = 90 |
b = 82.72 | β = 90 |
c = 465.317 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | PIXEL | DECTRIS PILATUS 6M | KB Mirrors | 2019-10-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALBA BEAMLINE XALOC | 0.979260 | ALBA | XALOC |
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 | 1.85 | 46.62 | 97.2 | 0.153 | 0.162 | 0.052 | 0.992 | 8 | 7.4 | 129847 |
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 | 1.86 | 1.89 | 80.7 | 0.658 | 0.768 | 0.377 | 0.568 | 1 | 3.2 |
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 | 6SRD | 1.86 | 46.62 | 123280 | 6472 | 95.69 | 0.2398 | 0.2385 | 0.2633 | RANDOM | 33.218 |
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] | |
-8.51 | -6.95 | 15.46 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.423 |
r_dihedral_angle_3_deg | 14.792 |
r_dihedral_angle_4_deg | 13.273 |
r_dihedral_angle_1_deg | 6.66 |
r_angle_refined_deg | 1.417 |
r_angle_other_deg | 1.24 |
r_chiral_restr | 0.081 |
r_bond_refined_d | 0.006 |
r_bond_other_d | 0.004 |
r_gen_planes_refined | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 12535 |
Nucleic Acid Atoms | |
Solvent Atoms | 194 |
Heterogen Atoms | 184 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |