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PanDDA analysis group deposition -- SARS-CoV-2 Nsp1 in complex with fragment C06 from the F2X-Entry library
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EQ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M HEPES pH 7.5 and 25% (w/v) PEG 3350. Reproducibility was improved by seeding.
Crystal Properties Matthews coefficient Solvent content 1.88 34.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.767 α = 90 b = 36.767 β = 90 c = 142.725 γ = 90
Symmetry Space Group P 43 21 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 6M 2023-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 1.52 36.77 100 0.055 0.058 0.017 1 15.5 11.6 16041
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 1.52 1.55 100 2.742 2.876 0.858 0.36 11
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.52 35.71 14897 788 98.18 0.21209 0.21064 0.24151 0.221 RANDOM 34.987
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] 0.37 0.37 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.322 r_dihedral_angle_3_deg 14.391 r_dihedral_angle_4_deg 13.62 r_dihedral_angle_1_deg 7.053 r_long_range_B_refined 6.99 r_long_range_B_other 6.924 r_scangle_other 5.128 r_mcangle_it 3.475 r_mcangle_other 3.474 r_scbond_it 2.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.322 r_dihedral_angle_3_deg 14.391 r_dihedral_angle_4_deg 13.62 r_dihedral_angle_1_deg 7.053 r_long_range_B_refined 6.99 r_long_range_B_other 6.924 r_scangle_other 5.128 r_mcangle_it 3.475 r_mcangle_other 3.474 r_scbond_it 2.974 r_scbond_other 2.972 r_mcbond_other 2.289 r_mcbond_it 2.286 r_angle_refined_deg 1.448 r_angle_other_deg 1.237 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 873 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PHASER phasing DIALS data scaling DIALS data reduction