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Macro domain of SARS-CoV-2 in complex with ADP-ribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ACF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 283 37.5% precipitant mix (stock: 2.5% MPD, 25% PEG1000, 25% PEG3350), 0.1M pH 8.5 buffer mix (1M Tris, 1M Bicine) and 0.1M carboxylic acids mix (0.2M sodium formate, 0.2M ammonium acetate, 0.2M sodium citrate, 0.2M sodium potassium, 0.2M sodium oxamate)
Crystal Properties Matthews coefficient Solvent content 3.52 65.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.993 α = 90 b = 85.993 β = 90 c = 143.567 γ = 90
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 MX300-HS 2020-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.99984 NSRRC TPS 05A
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 3.83 29.74 97.7 0.163 0.186 0.087 0.9009 7.68 3.5 9363 37.84
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.83 3.97 91.7 0.583 0.717 0.41
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2ACF 3.83 29.74 1.34 9352 919 92.56 0.2382 0.2349 0.2338 0.2682 0.2642 RANDOM 26.76
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 7.2257 f_angle_d 1.3351 f_chiral_restr 0.0545 f_bond_d 0.0179 f_plane_restr 0.0062
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4846 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 144
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing