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Structure of C. elegans ZK177.8, SAMHD1 ortholog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BZB PDB entry 4BZB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8 298 0.1 M SPG, pH 5.5, 20% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.72 54.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.681 α = 65.58 b = 90.557 β = 65.49 c = 93.357 γ = 86.22
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 EIGER X 16M 2019-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.987 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.8 50 94.1 0.099 0.129 0.082 9.8 2 209546
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 1.8 1.83 91.3 0.728 0.956 0.614 0.163 2
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 4BZB 1.81 46.03 198955 10556 93.44 0.1835 0.1822 0.1882 0.2089 0.2123 RANDOM 30.921
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] -0.36 -0.1 -0.02 -0.07 -0.1 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.221 r_dihedral_angle_4_deg 18.565 r_dihedral_angle_3_deg 14.914 r_dihedral_angle_1_deg 5.925 r_angle_refined_deg 1.704 r_angle_other_deg 1.44 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.221 r_dihedral_angle_4_deg 18.565 r_dihedral_angle_3_deg 14.914 r_dihedral_angle_1_deg 5.925 r_angle_refined_deg 1.704 r_angle_other_deg 1.44 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16225 Nucleic Acid Atoms Solvent Atoms 1482 Heterogen Atoms 420
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction BUCCANEER phasing