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PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with Z760048004
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.14 298 25% PEG 3350, 0.1M Tris, 0.2M Ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.37 48.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.821 α = 90 b = 60.61 β = 90 c = 146.759 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M 2023-01-26 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92124 Diamond I04-1
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 1.28 56.02 89.4 0.126 0.132 0.037 0.997 10.1 11.5 88583
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 1.28 1.3 45.7 3.202 3.499 1.363 0.343 6.3
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 1.28 56.08 84203 2925 87.73 0.23496 0.23475 0.2425 0.23973 0.2493 RANDOM 19.659
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] -0.84 0.45 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.2 r_dihedral_angle_4_deg 15.27 r_dihedral_angle_3_deg 14.1 r_long_range_B_other 11.879 r_long_range_B_refined 11.872 r_dihedral_angle_1_deg 7.343 r_scangle_other 4.712 r_scbond_it 2.93 r_scbond_other 2.929 r_mcangle_other 2.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.2 r_dihedral_angle_4_deg 15.27 r_dihedral_angle_3_deg 14.1 r_long_range_B_other 11.879 r_long_range_B_refined 11.872 r_dihedral_angle_1_deg 7.343 r_scangle_other 4.712 r_scbond_it 2.93 r_scbond_other 2.929 r_mcangle_other 2.912 r_mcangle_it 2.911 r_angle_refined_deg 1.957 r_mcbond_other 1.916 r_mcbond_it 1.912 r_angle_other_deg 1.432 r_chiral_restr 0.296 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2808 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction