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Muscovy duck circovirus Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WDZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 0.1 M sodium acetate, pH 4.8, 2.2M ammonium sulfate, 20% glycerol added to drop
Crystal Properties Matthews coefficient Solvent content 3.44 64.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.986 α = 90 b = 102.986 β = 90 c = 138.294 γ = 120
Symmetry Space Group P 61 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 2020-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97910 APS 24-ID-C
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 1.69 54.65 99.84 0.03628 0.03856 0.01275 1 32.89 8.7 48935 28.27
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 1.69 1.751 99.69 0.8253 0.8776 0.2922 0.784 2.28 8.5
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 THROUGHOUT 6WDZ 1.69 54.65 1.34 48924 2401 99.84 0.1718 0.1706 0.173 0.1946 0.1967 34.3287
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1570 Nucleic Acid Atoms 380 Solvent Atoms 281 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing PDB_EXTRACT data extraction Coot model building