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PanDDA analysis group deposition -- SARS-CoV-2 Nsp1 in complex with fragment D10 from the F2X-Entry 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 33.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.693 α = 90 b = 36.693 β = 90 c = 142.008 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 1.38 36.69 100 0.065 0.068 0.02 1 13.4 11.7 21045
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 1.38 1.4 100 2.781 2.915 0.861 0.356 11.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.38 35.55 19639 1003 98.32 0.20391 0.20275 0.2116 0.22656 0.2358 RANDOM 27.224
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.382 r_dihedral_angle_3_deg 13.797 r_dihedral_angle_4_deg 9.032 r_dihedral_angle_1_deg 7.292 r_long_range_B_refined 6.838 r_long_range_B_other 6.835 r_scangle_other 5.186 r_mcangle_it 3.244 r_mcangle_other 3.242 r_scbond_it 2.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.382 r_dihedral_angle_3_deg 13.797 r_dihedral_angle_4_deg 9.032 r_dihedral_angle_1_deg 7.292 r_long_range_B_refined 6.838 r_long_range_B_other 6.835 r_scangle_other 5.186 r_mcangle_it 3.244 r_mcangle_other 3.242 r_scbond_it 2.997 r_scbond_other 2.995 r_mcbond_other 2.078 r_mcbond_it 2.074 r_angle_refined_deg 1.614 r_angle_other_deg 1.312 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 82 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement PHASER phasing DIALS data scaling DIALS data reduction