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PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with Z401437758
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 49.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.868 α = 90 b = 62.332 β = 90 c = 148.075 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) 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 1.607 74.037 71.8 0.336 0.352 0.105 5.6 10.5 37747
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.607 1.726 19 3.097 3.257 0.994 10
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 1.61 74.04 35867 1880 71.73 0.19492 0.19327 0.2132 0.22701 0.2471 RANDOM 21.546
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] 0.08 -0.06 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.793 r_dihedral_angle_4_deg 17.707 r_dihedral_angle_3_deg 16.32 r_dihedral_angle_1_deg 7.265 r_long_range_B_refined 6.434 r_long_range_B_other 6.224 r_scangle_other 3.603 r_mcangle_other 2.65 r_mcangle_it 2.648 r_scbond_it 2.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.793 r_dihedral_angle_4_deg 17.707 r_dihedral_angle_3_deg 16.32 r_dihedral_angle_1_deg 7.265 r_long_range_B_refined 6.434 r_long_range_B_other 6.224 r_scangle_other 3.603 r_mcangle_other 2.65 r_mcangle_it 2.648 r_scbond_it 2.15 r_scbond_other 2.15 r_mcbond_other 1.628 r_mcbond_it 1.618 r_angle_refined_deg 1.455 r_angle_other_deg 1.289 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 310 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction