☰ Navigation Tabs
Crystal structure of tetrameric human wt-SAMHD1 (residues 109-626) with GTP, dATP, dTMPNPP and Mg
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TXA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.1 M Bistris methane-HCl pH 6, 19% (w/v) PEG 3350, 0.15 M Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.39 48.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.482 α = 90 b = 172.232 β = 95.31 c = 275.271 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 PILATUS 6M-F 2017-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 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 3.186 91.364 91.364 0.433 0.467 0.175 0.96 4.7 7 80315 50.1
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 3.186 3.63 76.2 1.161 1.257 0.476 0.668 1.7 6.7
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 6TXA 3.19 91.22 76240 4073 53.35 0.2196 0.2179 0.2193 0.2518 0.2507 RANDOM 64.692
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] -1.33 0.62 3.52 -2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.696 r_dihedral_angle_4_deg 15.255 r_dihedral_angle_3_deg 14.018 r_dihedral_angle_1_deg 5.502 r_angle_refined_deg 1.411 r_angle_other_deg 1.008 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.696 r_dihedral_angle_4_deg 15.255 r_dihedral_angle_3_deg 14.018 r_dihedral_angle_1_deg 5.502 r_angle_refined_deg 1.411 r_angle_other_deg 1.008 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 61116 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1559
Software Software Software Name Purpose XDS data reduction Aimless data scaling STARANISO data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction