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PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with Z281773378
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 49.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.744 α = 90 b = 62.831 β = 90 c = 147.409 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 2023-01-28 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 1.37 62.82 99.7 0.082 0.086 0.024 0.999 10.4 11.9 84211
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 1.37 1.4 94.8 2.226 2.397 0.864 0.36 7.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.37 57.87 75808 3016 93.45 0.19452 0.19378 0.20941 0.2156 RANDOM 24.997
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] -0.23 0.06 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.026 r_dihedral_angle_4_deg 14.646 r_dihedral_angle_3_deg 14.277 r_long_range_B_refined 7.731 r_long_range_B_other 7.564 r_dihedral_angle_1_deg 7.272 r_scangle_other 5.878 r_mcangle_other 3.584 r_mcangle_it 3.576 r_scbond_it 3.573
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.026 r_dihedral_angle_4_deg 14.646 r_dihedral_angle_3_deg 14.277 r_long_range_B_refined 7.731 r_long_range_B_other 7.564 r_dihedral_angle_1_deg 7.272 r_scangle_other 5.878 r_mcangle_other 3.584 r_mcangle_it 3.576 r_scbond_it 3.573 r_scbond_other 3.572 r_mcbond_it 2.317 r_mcbond_other 2.306 r_angle_refined_deg 1.701 r_angle_other_deg 1.404 r_chiral_restr 0.085 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 320 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction