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PanDDA analysis group deposition -- SARS-CoV-2 Nsp1 crystal D04 (dataset 1) from the KIT 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 34.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.68 α = 90 b = 36.68 β = 90 c = 142.29 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 2023-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 1.68 35.54 11280 581 99.96 0.19927 0.1969 0.24188 0.2044 RANDOM 35.821
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] 0.14 0.14 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.815 r_dihedral_angle_3_deg 12.574 r_dihedral_angle_4_deg 8.257 r_long_range_B_refined 8.191 r_long_range_B_other 8.146 r_dihedral_angle_1_deg 7.591 r_scangle_other 6.385 r_scbond_it 4.148 r_scbond_other 4.144 r_mcangle_other 3.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.815 r_dihedral_angle_3_deg 12.574 r_dihedral_angle_4_deg 8.257 r_long_range_B_refined 8.191 r_long_range_B_other 8.146 r_dihedral_angle_1_deg 7.591 r_scangle_other 6.385 r_scbond_it 4.148 r_scbond_other 4.144 r_mcangle_other 3.925 r_mcangle_it 3.915 r_mcbond_it 2.802 r_mcbond_other 2.782 r_angle_refined_deg 1.537 r_angle_other_deg 1.35 r_chiral_restr 0.073 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 873 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHASER phasing XDS data scaling XDS data reduction xdsapp data scaling xdsapp data reduction