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Crystal structure of tetrameric human wt-SAMHD1 (residues 109-626) with GTP, dATP, dCMPNPP 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, 17% (w/v) PEG 3350, 0.15 M Li2SO4.
Crystal Properties Matthews coefficient Solvent content 2.49 50.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.113 α = 90 b = 175.239 β = 94.81 c = 277.269 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 6M 2017-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 2.84 276.291 93.7 0.169 0.195 0.097 0.991 7.1 3.9 161935 46.2
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 2.84 3.1 53.8 0.885 1.016 0.494 0.595 1.5 4.1
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 2.84 276.291 153495 8049 72.74 0.229 0.228 0.2272 0.2489 0.2472 RANDOM 52.052
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] -1.92 -1.44 0.47 1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.955 r_dihedral_angle_3_deg 15.57 r_dihedral_angle_4_deg 15.357 r_dihedral_angle_1_deg 5.581 r_angle_refined_deg 1.702 r_angle_other_deg 0.993 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.955 r_dihedral_angle_3_deg 15.57 r_dihedral_angle_4_deg 15.357 r_dihedral_angle_1_deg 5.581 r_angle_refined_deg 1.702 r_angle_other_deg 0.993 r_chiral_restr 0.087 r_bond_refined_d 0.013 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 60407 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1543
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling STARANISO data scaling PHASER phasing PDB_EXTRACT data extraction