7A5Y

Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with Rp-dGTP-alphaS (T8T) and Mg


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6TX0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62930.1 M Bistris methane-HCl pH 6, 15% (w/v) PEG 3350, 0.15 M Li2SO4
Crystal Properties
Matthews coefficientSolvent content
2.1643.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.193α = 90
b = 181.263β = 90
c = 286.331γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2020-01-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.29153.1592.60.2650.2870.110.9896.36.714590030.7
Highest Resolution Shell
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)RedundancyNumber Unique Reflections (All)
12.292.4557.61.5361.6680.6460.5461.66.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6TX02.29153.15138594732677.170.21170.21010.2403RANDOM37.524
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]
-1.40.670.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.681
r_dihedral_angle_4_deg17.177
r_dihedral_angle_3_deg16.878
r_dihedral_angle_1_deg5.973
r_angle_refined_deg1.915
r_angle_other_deg1.083
r_chiral_restr0.11
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.681
r_dihedral_angle_4_deg17.177
r_dihedral_angle_3_deg16.878
r_dihedral_angle_1_deg5.973
r_angle_refined_deg1.915
r_angle_other_deg1.083
r_chiral_restr0.11
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms29346
Nucleic Acid Atoms
Solvent Atoms343
Heterogen Atoms776

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction