Crystal structure of SAMHD1 dimer bound to an inhibitor obtained from high-throughput chemical tethering to the guanine antiviral acyclovir
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6U6Z |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293.15 | Apo DELTA 112- SAMHD1 crystals were obtained by the hanging drop method using 1 micro L of 5 mg/mL Delta 112-SAMHD1 (10 mM Tris-HCl pH 8.0, 150 mM NaCl, 4 mM MgCl2, 0.5 mM TCEP) and 2 L 17% PEG3350, 0.15 M Ammonium citrate pH 7.3. Drops were placed in 20 degrees C for over a week, and large crystal rods and plates were observed |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.62 | 53.05 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.347 | α = 73.047 |
b = 94.274 | β = 71.481 |
c = 96.579 | γ = 65.203 |
Symmetry | |
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Space Group | P 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 | The beamline has an adaptable optical system consisting of white beam slits, a double crystal Si(111) monochromator with horizontal axis, tandem flat beam deflecting mirrors (Pd coating), and Kirkpatrick-Baez focusing mirrors, which are Pd coated and able to bend adaptively using 16 piezo actuators. Each optical element is preceded by slits and its transmitted beam is monitored by beam position monitors or retractable screens. | 2024-08-22 | 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 | 0.9201 | NSLS-II | 17-ID-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.72 | 34.01 | 99 | 0.149 | 0.064 | 0.997 | 8.5 | 6.4 | 64250 | 65.72 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.72 | 2.87 | 98.5 | 0.497 | 1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.72 | 33.65 | 1.96 | 64057 | 3133 | 98.74 | 0.19 | 0.1878 | 0.1875 | 0.2342 | 0.2317 | 80.61 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 18.2347 |
f_angle_d | 1.0682 |
f_chiral_restr | 0.0629 |
f_bond_d | 0.0108 |
f_plane_restr | 0.0094 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14465 |
Nucleic Acid Atoms | |
Solvent Atoms | 74 |
Heterogen Atoms | 156 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
autoPROC | data reduction |
Aimless | data scaling |
MOLREP | phasing |