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PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with Z56978034
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 2.47 50.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.809 α = 90 b = 62.789 β = 90 c = 147.786 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 1.25 38.76 91.9 0.065 0.068 0.019 0.999 14.3 10.8 101816
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 1.25 1.27 52.7 1.469 1.699 0.835 0.328 3.9
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 1.25 38.79 97323 3013 90.42 0.18763 0.18714 0.2027 0.19791 0.2127 RANDOM 23.272
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 0.11 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.684 r_dihedral_angle_3_deg 15.474 r_dihedral_angle_4_deg 14.262 r_long_range_B_refined 8.499 r_long_range_B_other 8.404 r_dihedral_angle_1_deg 7.479 r_scangle_other 6.53 r_scbond_it 3.902 r_scbond_other 3.901 r_mcangle_other 3.679
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.684 r_dihedral_angle_3_deg 15.474 r_dihedral_angle_4_deg 14.262 r_long_range_B_refined 8.499 r_long_range_B_other 8.404 r_dihedral_angle_1_deg 7.479 r_scangle_other 6.53 r_scbond_it 3.902 r_scbond_other 3.901 r_mcangle_other 3.679 r_mcangle_it 3.671 r_mcbond_other 2.269 r_mcbond_it 2.254 r_angle_refined_deg 1.851 r_angle_other_deg 1.431 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 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 2800 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction