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Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with XTP, dAMPNPP and Mn
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, 14% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.24 45.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.978 α = 90 b = 104.978 β = 90 c = 195.516 γ = 90
Symmetry Space Group P 43 21 2
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 6M 2017-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.97866 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 2.25 71.59 97.75 0.122 0.126 0.029 0.998 14.5 16.83 51603 37.6
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 2.25 2.29 80.13 1.216 1.307 0.463 0.673 1.8 6.84
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 2.25 71.51 48696 2568 97.42 0.1974 0.1952 0.1999 0.2388 0.2407 RANDOM 47.142
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] 0.17 0.17 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.701 r_dihedral_angle_4_deg 16.929 r_dihedral_angle_3_deg 15.242 r_dihedral_angle_1_deg 5.942 r_angle_refined_deg 2.095 r_angle_other_deg 1.14 r_chiral_restr 0.122 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.701 r_dihedral_angle_4_deg 16.929 r_dihedral_angle_3_deg 15.242 r_dihedral_angle_1_deg 5.942 r_angle_refined_deg 2.095 r_angle_other_deg 1.14 r_chiral_restr 0.122 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7748 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 192
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction