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PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with Z385450668
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 2.45 49.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.744 α = 90 b = 62.5 β = 90 c = 147.471 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 1.47 62.5 99.9 0.116 0.121 0.034 0.998 7.9 12.6 68128
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 1.47 1.5 97.6 1.951 2.065 0.663 0.309 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 1.47 57.61 62588 3010 96.38 0.20308 0.20199 0.2274 0.22434 0.2424 RANDOM 24.087
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] -0.54 0.2 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.459 r_dihedral_angle_4_deg 17.961 r_dihedral_angle_3_deg 14.965 r_dihedral_angle_1_deg 7.337 r_long_range_B_refined 6.207 r_long_range_B_other 6.126 r_scangle_other 4.574 r_mcangle_other 3.094 r_mcangle_it 3.086 r_scbond_it 2.745
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.459 r_dihedral_angle_4_deg 17.961 r_dihedral_angle_3_deg 14.965 r_dihedral_angle_1_deg 7.337 r_long_range_B_refined 6.207 r_long_range_B_other 6.126 r_scangle_other 4.574 r_mcangle_other 3.094 r_mcangle_it 3.086 r_scbond_it 2.745 r_scbond_other 2.745 r_mcbond_it 1.951 r_mcbond_other 1.943 r_angle_refined_deg 1.583 r_angle_other_deg 1.383 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 2808 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction