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PanDDA analysis group deposition -- SARS-CoV-2 Nsp1 in complex with fragment X5449 (well G01) from the KIT 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 1.85 33.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.63 α = 90 b = 36.63 β = 90 c = 141.95 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
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.88 35.49 100 0.076 0.08 0.9990000000000001 18.96 8535
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.99 99.9 1.0090000000000001 1.05 0.7559999999999999
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 1.88 35.49 8108 427 99.96 0.19578 0.19405 0.1997 0.2306 0.2338 RANDOM 38.997
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] -0.43 -0.43 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.508 r_dihedral_angle_3_deg 14.988 r_long_range_B_refined 9.177 r_long_range_B_other 9.173 r_dihedral_angle_4_deg 7.71 r_dihedral_angle_1_deg 7.104 r_scangle_other 6.155 r_mcangle_it 4.21 r_mcangle_other 4.207 r_scbond_it 3.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.508 r_dihedral_angle_3_deg 14.988 r_long_range_B_refined 9.177 r_long_range_B_other 9.173 r_dihedral_angle_4_deg 7.71 r_dihedral_angle_1_deg 7.104 r_scangle_other 6.155 r_mcangle_it 4.21 r_mcangle_other 4.207 r_scbond_it 3.628 r_scbond_other 3.625 r_mcbond_other 2.875 r_mcbond_it 2.867 r_angle_refined_deg 1.55 r_angle_other_deg 1.274 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 82 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PHASER phasing XDS data scaling XDS data reduction