5OXD
Complex of a C. perfringens O-GlcNAcase with a fragment hit
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293.15 | Apo crystals were grown in 0.6 M NaAcetate pH 7.5, 0.175 M cadmium sulphate (ML). Crystals were then transferred into a drop supplemented with 10 mM ligand and incubated for 4 h. Crystals were cryo-protected by short immersion in ML supplemented with 20% glycerol and saturated with ligand. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.46 | 72.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 117.794 | α = 90 |
b = 117.794 | β = 90 |
c = 147.233 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 EIGER X 4M | 2017-08-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-3 | 0.9678 | ESRF | MASSIF-3 |
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 | 2.6 | 50.01 | 99.1 | 0.222 | 0.254 | 0.122 | 0.993 | 7.9 | 7.9 | 35270 |
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 | 2.6 | 2.72 | 99.5 | 2.38 | 2.704 | 0.1273 | 0.7 | 1 | 8.2 |
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 | 2YDS | 2.6 | 50.01 | 33390 | 1880 | 99.06 | 0.17436 | 0.17174 | 0.22061 | RANDOM | 62.48 |
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] | |
2.15 | 1.07 | 2.15 | -6.97 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 43.134 |
r_dihedral_angle_4_deg | 17.58 |
r_dihedral_angle_3_deg | 17.532 |
r_long_range_B_refined | 10.522 |
r_long_range_B_other | 10.522 |
r_scangle_other | 8.657 |
r_dihedral_angle_1_deg | 7.113 |
r_mcangle_it | 6.492 |
r_mcangle_other | 6.491 |
r_scbond_it | 5.691 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4586 |
Nucleic Acid Atoms | |
Solvent Atoms | 71 |
Heterogen Atoms | 33 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |