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Human ARTD2 in complex with DNA oligonucleotides
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DSY F6IK and 5DSY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 Sample was crystallized in 0.1 M MES pH 6.5 and 1 M ammonium sulfate.
Cryo solution was a mixture of 10% (v/v) glycerol, 10% (v/v) diethylene glycol, and 10% (v/v) 2-propanol with the crystallization conditions
Crystal Properties Matthews coefficient Solvent content 3.6 67.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.83 α = 90 b = 166.83 β = 90 c = 143.84 γ = 90
Symmetry Space Group I 41 2 2
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 S 6M 2019-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9687 Diamond I24
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 2.8 50 98.9 0.111 0.12 0.99 9.25 6.8 24990 98.91
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 2.8 2.87 99.6 1.43 1.56 0.44 1.59 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE F6IK and 5DSY 2.8 26.84 1.33 24978 1175 99.04 0.2287 0.2267 0.2282 0.2707 0.2704 142.96
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 21.1143 f_angle_d 0.7387 f_chiral_restr 0.0432 f_bond_d 0.0053 f_plane_restr 0.0039
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3606 Nucleic Acid Atoms 654 Solvent Atoms Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling MrBUMP phasing