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PanDDA analysis group deposition -- SARS-CoV-2 Nsp1 crystal D07a (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 1.88 34.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.718 α = 90 b = 36.718 β = 90 c = 143.061 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 1.59 36.72 100 0.129 0.136 0.04 0.998 6.5 11.2 14077
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 1.59 1.62 100 3.087 3.226 0.927 0.307 11.8
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 1.59 35.79 10781 553 81.38 0.22195 0.21841 0.23 0.28509 0.2109 RANDOM 38.101
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] -0.57 -0.57 1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.657 r_dihedral_angle_3_deg 13.746 r_dihedral_angle_4_deg 11.188 r_long_range_B_other 9.921 r_long_range_B_refined 9.892 r_dihedral_angle_1_deg 8.011 r_scangle_other 6.979 r_mcangle_other 4.549 r_mcangle_it 4.545 r_scbond_it 4.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.657 r_dihedral_angle_3_deg 13.746 r_dihedral_angle_4_deg 11.188 r_long_range_B_other 9.921 r_long_range_B_refined 9.892 r_dihedral_angle_1_deg 8.011 r_scangle_other 6.979 r_mcangle_other 4.549 r_mcangle_it 4.545 r_scbond_it 4.248 r_scbond_other 4.244 r_mcbond_it 3.049 r_mcbond_other 3.038 r_angle_refined_deg 1.548 r_angle_other_deg 1.204 r_chiral_restr 0.064 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
Software Software Software Name Purpose REFMAC refinement PHASER phasing DIALS data scaling DIALS data reduction