6DWJ
SAMHD1 Bound to Vidarabine-TP in the Catalytic Pocket
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 298 | 100 MM BIS-TRIS PH 6.7 AND 25% (W/V) PEG1500 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.28 | 45.99 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 86.862 | ¦Á = 90 |
b = 146.724 | ¦Â = 114.45 |
c = 99.594 | ¦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 | PIXEL | DECTRIS EIGER X 9M | 2018-01-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 17-ID-1 | 0.92014 | NSLS-II | 17-ID-1 |
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 | 2.5 | 50 | 97.4 | 0.107 | 0.989 | 10 | 3.5 | 75598 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.5 | 2.54 | 97.1 | 0.737 | 0.688 | 3.3 |
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 | THROUGHOUT | 2.5 | 50 | 71792 | 3793 | 96.26 | 0.17701 | 0.17533 | 0.20792 | RANDOM | 72.623 |
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] | |
-3.82 | 2 | -0.95 | 2.08 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.015 |
r_dihedral_angle_3_deg | 17.758 |
r_dihedral_angle_4_deg | 15.902 |
r_long_range_B_refined | 8.694 |
r_long_range_B_other | 8.694 |
r_dihedral_angle_1_deg | 5.48 |
r_scangle_other | 4.986 |
r_mcangle_it | 4.346 |
r_mcangle_other | 4.346 |
r_scbond_it | 3.19 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15732 |
Nucleic Acid Atoms | |
Solvent Atoms | 156 |
Heterogen Atoms | 409 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |