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PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with Z44548882
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 2.49 50.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.854 α = 90 b = 62.861 β = 90 c = 148.557 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 2023-01-28 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 1.35 38.9 98.3 0.073 0.076 0.021 0.999 11.8 11.8 87571
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 1.35 1.37 87.5 1.882 2.047 0.771 0.331 6.6
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 1.35 38.93 79816 3007 92.97 0.19221 0.19143 0.2039 0.20832 0.2188 RANDOM 24.963
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] -0.23 -0.15 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.437 r_dihedral_angle_4_deg 16.977 r_dihedral_angle_3_deg 14.525 r_long_range_B_refined 8.219 r_long_range_B_other 8.087 r_dihedral_angle_1_deg 7.399 r_scangle_other 6.119 r_mcangle_it 3.74 r_mcangle_other 3.74 r_scbond_it 3.667
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.437 r_dihedral_angle_4_deg 16.977 r_dihedral_angle_3_deg 14.525 r_long_range_B_refined 8.219 r_long_range_B_other 8.087 r_dihedral_angle_1_deg 7.399 r_scangle_other 6.119 r_mcangle_it 3.74 r_mcangle_other 3.74 r_scbond_it 3.667 r_scbond_other 3.666 r_mcbond_other 2.366 r_mcbond_it 2.318 r_angle_refined_deg 1.72 r_angle_other_deg 1.369 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 2800 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction