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PanDDA analysis group deposition -- SARS-CoV-2 Nsp1 in complex with fragment X7214 (well H02) 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 1.86 33.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.65 α = 90 b = 36.65 β = 90 c = 142.37 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 1.79 35.49 100 0.079 0.083 1 19.18 9866
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 1.79 1.9 100 2.311 2.416 0.419
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 1.79 35.49 9372 494 99.99 0.208 0.20566 0.2117 0.25419 0.2504 RANDOM 38.819
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] 0.33 0.33 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.887 r_dihedral_angle_4_deg 13.842 r_dihedral_angle_3_deg 13.247 r_long_range_B_refined 8.553 r_long_range_B_other 8.55 r_dihedral_angle_1_deg 6.892 r_scangle_other 5.511 r_mcangle_it 3.918 r_mcangle_other 3.916 r_scbond_it 3.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.887 r_dihedral_angle_4_deg 13.842 r_dihedral_angle_3_deg 13.247 r_long_range_B_refined 8.553 r_long_range_B_other 8.55 r_dihedral_angle_1_deg 6.892 r_scangle_other 5.511 r_mcangle_it 3.918 r_mcangle_other 3.916 r_scbond_it 3.327 r_scbond_other 3.326 r_mcbond_other 2.459 r_mcbond_it 2.455 r_angle_refined_deg 1.417 r_angle_other_deg 1.247 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.003 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 14
Software Software Software Name Purpose REFMAC refinement PHASER phasing XDS data scaling XDS data reduction