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PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with POB0050
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 49.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.819 α = 90 b = 62.651 β = 90 c = 147.515 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 2023-01-27 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 1.57 62.64 99.8 0.19 0.198 0.054 0.997 9.3 13.3 56255
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 1.57 1.6 95 4.57 4.781 1.389 0.376 11.5
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 1.57 57.73 53188 2725 99.32 0.19507 0.19394 0.2077 0.21685 0.229 RANDOM 25.1
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] -0.1 -0.18 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.788 r_dihedral_angle_4_deg 14.702 r_dihedral_angle_3_deg 13.599 r_dihedral_angle_1_deg 7.11 r_long_range_B_refined 7.023 r_long_range_B_other 6.961 r_scangle_other 4.824 r_mcangle_other 3.189 r_mcangle_it 3.186 r_scbond_it 2.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.788 r_dihedral_angle_4_deg 14.702 r_dihedral_angle_3_deg 13.599 r_dihedral_angle_1_deg 7.11 r_long_range_B_refined 7.023 r_long_range_B_other 6.961 r_scangle_other 4.824 r_mcangle_other 3.189 r_mcangle_it 3.186 r_scbond_it 2.986 r_scbond_other 2.985 r_mcbond_it 2.131 r_mcbond_other 2.124 r_angle_refined_deg 1.555 r_angle_other_deg 1.408 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 312 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction