9EC2 | pdb_00009ec2

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)
TypeSourceAccession CodeDetails
experimental modelPDB 6U6Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293.15Apo 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
Matthews coefficientSolvent content
2.6253.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.347α = 73.047
b = 94.274β = 71.481
c = 96.579γ = 65.203
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9MThe 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.2024-08-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-10.9201NSLS-II17-ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.7234.01990.1490.0640.9978.56.46425065.72
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.722.8798.50.4971

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.7233.651.9664057313398.740.190.18780.18750.23420.231780.61
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.2347
f_angle_d1.0682
f_chiral_restr0.0629
f_bond_d0.0108
f_plane_restr0.0094
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14465
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms156

Software

Software
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing