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Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with Rp-dGTP-alphaS (T8T) and Mg
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TX0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.1 M Bistris methane-HCl pH 6, 15% (w/v) PEG 3350, 0.15 M Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.16 43.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.193 α = 90 b = 181.263 β = 90 c = 286.331 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2020-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.29 153.15 92.6 0.265 0.287 0.11 0.989 6.3 6.7 145900 30.7
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) Redundancy Number Unique Reflections (All) 1 2.29 2.45 57.6 1.536 1.668 0.646 0.546 1.6 6.5
Refinement Statistics 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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6TX0 2.29 153.15 138594 7326 77.17 0.2117 0.2101 0.2141 0.2403 0.2417 RANDOM 37.524
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] -1.4 0.67 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.681 r_dihedral_angle_4_deg 17.177 r_dihedral_angle_3_deg 16.878 r_dihedral_angle_1_deg 5.973 r_angle_refined_deg 1.915 r_angle_other_deg 1.083 r_chiral_restr 0.11 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.681 r_dihedral_angle_4_deg 17.177 r_dihedral_angle_3_deg 16.878 r_dihedral_angle_1_deg 5.973 r_angle_refined_deg 1.915 r_angle_other_deg 1.083 r_chiral_restr 0.11 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29346 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 776
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction