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Structure of recombinant human DNase1L3 in complex with Mg2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DNK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 283 19% PEG 8000,
250 mM Magnesium Chloride,
100 mM Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.17 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.313 α = 85.394 b = 72.671 β = 80.558 c = 73.169 γ = 88.392
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX325HE 2019-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.12709 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.21 32.07 94.9 0.145 0.153 0.998 8.5 9.1 50424 44.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 2.25 90.3 1.391 1.609 0.491 0.9 3.9
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 FREE R-VALUE 1DNK 2.22 32.06 49117 2221 93.95 0.1925 0.1906 0.1922 0.2304 0.2307 1 64.95
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.0088 f_angle_d 1.7385 f_chiral_restr 0.1227 f_bond_d 0.0152 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8700 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection XDS data scaling PHASER phasing Coot model building XDS data reduction