8QF2
Beta-L-Arabinofurano-cyclitol Aziridines are Cysteine-directed Broad-spectrum Inhibitors and Activity-based Probes for Retaining Beta-L-arabinofuranosidases
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7DIF |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 291 | 0.7 M sodium citrate, 0.1 M MES pH 6.5, 10 mM dithiothreitol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.95 | 58.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.26 | α = 90 |
b = 77.26 | β = 90 |
c = 254.647 | γ = 120 |
Symmetry | |
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Space Group | P 32 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 EIGER2 XE 16M | 2022-07-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97628 | Diamond | I03 |
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 | 2.35 | 85.03 | 100 | 0.199 | 0.995 | 7.7 | 20 | 37850 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.35 | 2.43 | 100 | 0.938 | 0.66 | 0.7 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.35 | 85.03 | 35892 | 1886 | 100 | 0.20933 | 0.20685 | 0.25426 | RANDOM | 69.408 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
1.63 | 0.82 | 1.63 | -5.3 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 15.215 |
r_dihedral_angle_2_deg | 10.304 |
r_long_range_B_refined | 9.968 |
r_long_range_B_other | 9.968 |
r_scangle_other | 8.38 |
r_mcangle_other | 8.271 |
r_mcangle_it | 8.266 |
r_dihedral_angle_1_deg | 6.9 |
r_mcbond_it | 6.147 |
r_mcbond_other | 6.144 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5096 |
Nucleic Acid Atoms | |
Solvent Atoms | 74 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
REFMAC | phasing |