☰ Navigation Tabs
PanDDA analysis group deposition -- SARS-CoV-2 Nsp1 in complex with fragment E01 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 1.87 34.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.723 α = 90 b = 36.723 β = 90 c = 142.204 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 1.49 36.72 100 0.077 0.081 0.024 0.999 9.9 11.5 16848
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 1.49 1.52 100 2.87 3.003 0.868 0.214 11.6
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 1.49 35.58 14176 708 88.63 0.20731 0.20631 0.2136 0.2267 0.2286 RANDOM 32.209
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 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.631 r_dihedral_angle_3_deg 13.964 r_dihedral_angle_4_deg 13.201 r_dihedral_angle_1_deg 6.955 r_long_range_B_refined 6.883 r_long_range_B_other 6.817 r_scangle_other 4.727 r_mcangle_it 3.231 r_mcangle_other 3.23 r_scbond_it 2.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.631 r_dihedral_angle_3_deg 13.964 r_dihedral_angle_4_deg 13.201 r_dihedral_angle_1_deg 6.955 r_long_range_B_refined 6.883 r_long_range_B_other 6.817 r_scangle_other 4.727 r_mcangle_it 3.231 r_mcangle_other 3.23 r_scbond_it 2.56 r_scbond_other 2.559 r_mcbond_other 1.832 r_mcbond_it 1.829 r_angle_refined_deg 1.399 r_angle_other_deg 1.228 r_chiral_restr 0.065 r_bond_refined_d 0.007 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 882 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PHASER phasing DIALS data scaling DIALS data reduction