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PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with Z1827602749
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 2.43 49.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.782 α = 90 b = 62.137 β = 90 c = 147.165 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 2023-01-25 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 1.49 38.49 99.7 0.268 0.28 0.08 0.996 12 12.4 65454
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 1.51 93.2 9.99 12.217 3.956 0.103 9.6
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 38.53 61652 3001 98.62 0.1858 0.18489 0.1961 0.20361 0.2116 RANDOM 22.802
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] -0.46 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.24 r_dihedral_angle_3_deg 13.744 r_dihedral_angle_4_deg 13.306 r_dihedral_angle_1_deg 7.314 r_long_range_B_refined 6.689 r_long_range_B_other 6.649 r_scangle_other 5.073 r_scbond_it 3.22 r_scbond_other 3.219 r_mcangle_other 3.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.24 r_dihedral_angle_3_deg 13.744 r_dihedral_angle_4_deg 13.306 r_dihedral_angle_1_deg 7.314 r_long_range_B_refined 6.689 r_long_range_B_other 6.649 r_scangle_other 5.073 r_scbond_it 3.22 r_scbond_other 3.219 r_mcangle_other 3.128 r_mcangle_it 3.124 r_mcbond_it 2.101 r_mcbond_other 2.093 r_angle_refined_deg 1.719 r_angle_other_deg 1.439 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 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 2808 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction