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Crystal Structure of the CoV-Y domain of SARS-CoV-2 Nonstructural Protein 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other MAD-phased seleno-methionine derivative
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 20%(w/v) PEG 3350,
0.18M Tri-Ammonium Citrate
Crystal Properties Matthews coefficient Solvent content 3.42 64.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.415 α = 90 b = 109.415 β = 90 c = 61.226 γ = 120
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 2020-07-09 M MAD 2 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2021-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97893, 0.97908, 0.97924 NSLS-II 17-ID-2 2 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97893 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.43 19.94 97.5 0.044 1 31.6 19.5 15488 85.87
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.43 2.47 1.8 0.922
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 FOURIER SYNTHESIS THROUGHOUT MAD-phased seleno-methionine derivative 2.43 19.94 15488 726 97.4 0.192 0.19 0.1981 0.232 0.2405 RANDOM 103.72
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] 23.4578 23.4578 -46.9156
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.31 t_omega_torsion 2.73 t_angle_deg 1.19 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.31 t_omega_torsion 2.73 t_angle_deg 1.19 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2164 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 36
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction autoPROC data scaling PHENIX phasing