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Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with XTP, dGMPNPP 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 2.41 49.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.782 α = 90 b = 172.897 β = 95.2 c = 275.886 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 S 6M 2017-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96861 Diamond I24
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 2.85 146.334 94.3 0.186 0.22 0.117 0.98 4 3.5 140978 49.5
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 2.853 3.201 67.3 0.577 0.684 0.364 0.729 1.5 3.4
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 2.853 146.243 133948 7029 66.44 0.1953 0.1944 0.1959 0.2118 0.2122 RANDOM 54.995
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] -0.24 -0.46 -0.53 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.776 r_dihedral_angle_4_deg 14.913 r_dihedral_angle_3_deg 13.656 r_dihedral_angle_1_deg 5.143 r_angle_refined_deg 1.535 r_angle_other_deg 1.034 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.776 r_dihedral_angle_4_deg 14.913 r_dihedral_angle_3_deg 13.656 r_dihedral_angle_1_deg 5.143 r_angle_refined_deg 1.535 r_angle_other_deg 1.034 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 61333 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1643
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling STARANISO data scaling PHASER phasing PDB_EXTRACT data extraction