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PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with Z839157334
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 2.44 49.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.802 α = 90 b = 62.317 β = 90 c = 147.363 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 1.3 147.44 94.4 0.074 0.077 0.022 0.999 11.5 11.4 92374
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 1.3 1.32 61.9 1.913 2.113 0.858 0.257 5.8
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 1.3 73.68 82448 2995 87.36 0.19969 0.19932 0.2102 0.2075 0.219 RANDOM 24.353
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 0.17 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.974 r_dihedral_angle_4_deg 16.2 r_dihedral_angle_3_deg 14.719 r_long_range_B_refined 9.178 r_long_range_B_other 9.14 r_dihedral_angle_1_deg 7.743 r_scangle_other 6.559 r_scbond_it 3.979 r_scbond_other 3.978 r_mcangle_it 3.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.974 r_dihedral_angle_4_deg 16.2 r_dihedral_angle_3_deg 14.719 r_long_range_B_refined 9.178 r_long_range_B_other 9.14 r_dihedral_angle_1_deg 7.743 r_scangle_other 6.559 r_scbond_it 3.979 r_scbond_other 3.978 r_mcangle_it 3.968 r_mcangle_other 3.967 r_mcbond_other 2.585 r_mcbond_it 2.555 r_angle_refined_deg 1.73 r_angle_other_deg 1.412 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 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 341 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction