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PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with Z1220452176
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 2.46 49.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.819 α = 90 b = 62.638 β = 90 c = 147.65 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 2023-01-24 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 1.42 57.66 97.5 0.097 0.104 0.036 0.996 9.7 7.9 74380
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 1.42 1.49 95 2.538 2.774 1.089 0.319 5.9
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 1.42 57.73 71157 2931 96.75 0.19214 0.19131 0.2021 0.20892 0.222 RANDOM 22.524
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] -0.29 0.55 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.082 r_dihedral_angle_3_deg 14.652 r_dihedral_angle_4_deg 14.054 r_dihedral_angle_1_deg 7.368 r_long_range_B_refined 6.3 r_long_range_B_other 6.263 r_scangle_other 4.755 r_mcangle_other 3.073 r_mcangle_it 3.065 r_scbond_it 2.971
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.082 r_dihedral_angle_3_deg 14.652 r_dihedral_angle_4_deg 14.054 r_dihedral_angle_1_deg 7.368 r_long_range_B_refined 6.3 r_long_range_B_other 6.263 r_scangle_other 4.755 r_mcangle_other 3.073 r_mcangle_it 3.065 r_scbond_it 2.971 r_scbond_other 2.97 r_mcbond_other 2.056 r_mcbond_it 2.049 r_angle_refined_deg 1.732 r_angle_other_deg 1.423 r_chiral_restr 0.087 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 336 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction