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PanDDA analysis group deposition -- SARS-CoV-2 Nsp1 crystal E04b (dataset 2) from the F2X-Entry library screening campaign, data used for ground state calculation
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 1.83 32.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.515 α = 90 b = 36.515 β = 90 c = 140.974 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 1.24 36.51 100 0.102 0.107 0.031 0.999 6.7 11.5 28228
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 1.24 1.26 100 4.275 4.473 1.297 0.297 11.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.24 35.37 19213 985 71.96 0.22695 0.22514 0.2262 0.26044 0.2405 RANDOM 25.148
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] 0.2 0.2 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.258 r_dihedral_angle_3_deg 14.452 r_dihedral_angle_4_deg 14.274 r_long_range_B_refined 11.644 r_long_range_B_other 11.581 r_dihedral_angle_1_deg 7.708 r_scangle_other 6.752 r_scbond_it 4.32 r_scbond_other 4.319 r_mcangle_it 3.432
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.258 r_dihedral_angle_3_deg 14.452 r_dihedral_angle_4_deg 14.274 r_long_range_B_refined 11.644 r_long_range_B_other 11.581 r_dihedral_angle_1_deg 7.708 r_scangle_other 6.752 r_scbond_it 4.32 r_scbond_other 4.319 r_mcangle_it 3.432 r_mcangle_other 3.429 r_mcbond_it 2.189 r_mcbond_other 2.189 r_angle_refined_deg 1.591 r_angle_other_deg 1.281 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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 868 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHASER phasing DIALS data scaling DIALS data reduction