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Crystal structure of the tetrameric dGTP-bound wild type SAMHD1 catalytic core
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3U1N PDB ENTRY 3U1N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.7 100 MM BIS-TRIS PH 6.7 AND 25% (W/V) PEG1500
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.002 α = 90 b = 138.727 β = 113.56 c = 93.715 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.88 50 95.6 0.12 8.2 2.9 40369 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.88 2.93 97.4 0.9 1.2 3
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 PDB ENTRY 3U1N 2.88 49.71 31009 1668 77.51 0.19307 0.19032 0.1929 0.2448 0.2426 RANDOM 66.501
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] 0.12 0.7 -1.99 1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.288 r_dihedral_angle_3_deg 17.639 r_dihedral_angle_4_deg 14.698 r_dihedral_angle_1_deg 5.316 r_mcangle_it 4.462 r_scbond_it 3.011 r_mcbond_it 2.721 r_mcbond_other 2.719 r_angle_refined_deg 1.673 r_angle_other_deg 1.289
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.288 r_dihedral_angle_3_deg 17.639 r_dihedral_angle_4_deg 14.698 r_dihedral_angle_1_deg 5.316 r_mcangle_it 4.462 r_scbond_it 3.011 r_mcbond_it 2.721 r_mcbond_other 2.719 r_angle_refined_deg 1.673 r_angle_other_deg 1.289 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.006 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15540 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 380
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing