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PanDDA analysis group deposition -- SARS-CoV-2 Nsp1 crystal Apo28 (dataset 1) 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 1.86 33.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.647 α = 90 b = 36.647 β = 90 c = 142.298 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 1.57 36.65 100 0.075 0.079 0.023 0.999 12.1 11.6 14479
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 1.57 1.6 100 4.095 4.291 1.266 0.211 11.3
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 1.57 35.6 13094 691 95.58 0.20562 0.20342 0.24534 0.1781 RANDOM 33.81
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] 0.27 0.27 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.883 r_dihedral_angle_3_deg 12.831 r_dihedral_angle_4_deg 9.44 r_long_range_B_refined 7.98 r_long_range_B_other 7.897 r_dihedral_angle_1_deg 7.482 r_scangle_other 5.842 r_mcangle_other 3.784 r_mcangle_it 3.766 r_scbond_it 3.752
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.883 r_dihedral_angle_3_deg 12.831 r_dihedral_angle_4_deg 9.44 r_long_range_B_refined 7.98 r_long_range_B_other 7.897 r_dihedral_angle_1_deg 7.482 r_scangle_other 5.842 r_mcangle_other 3.784 r_mcangle_it 3.766 r_scbond_it 3.752 r_scbond_other 3.748 r_mcbond_it 2.649 r_mcbond_other 2.617 r_angle_refined_deg 1.492 r_angle_other_deg 1.306 r_chiral_restr 0.071 r_bond_refined_d 0.008 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 873 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHASER phasing DIALS data scaling DIALS data reduction