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PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with Z667925512
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 = 42.762 α = 90 b = 62.598 β = 90 c = 147.83 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 1.41 38.72 98.9 0.102 0.106 0.029 0.999 9.3 12.4 76745
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 1.41 1.43 94.1 2.486 2.639 0.869 0.336 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.41 38.75 69176 2993 93.01 0.19112 0.1903 0.20753 0.2104 RANDOM 25.167
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] -0.22 0.55 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.664 r_dihedral_angle_4_deg 18.531 r_dihedral_angle_3_deg 14.482 r_long_range_B_refined 7.331 r_dihedral_angle_1_deg 7.301 r_long_range_B_other 7.27 r_scangle_other 5.121 r_mcangle_other 3.457 r_mcangle_it 3.452 r_scbond_it 3.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.664 r_dihedral_angle_4_deg 18.531 r_dihedral_angle_3_deg 14.482 r_long_range_B_refined 7.331 r_dihedral_angle_1_deg 7.301 r_long_range_B_other 7.27 r_scangle_other 5.121 r_mcangle_other 3.457 r_mcangle_it 3.452 r_scbond_it 3.101 r_scbond_other 3.1 r_mcbond_other 2.219 r_mcbond_it 2.21 r_angle_refined_deg 1.612 r_angle_other_deg 1.376 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 313 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction