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PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with NCL-00025345
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 2.45 49.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.674 α = 90 b = 62.447 β = 90 c = 147.803 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 1.51 38.68 98.3 0.096 0.1 0.027 0.999 9.2 13.2 61581
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 1.51 1.54 94.9 2.542 2.672 0.804 0.228 10.6
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 1.51 38.71 56221 2792 94.07 0.1986 0.19743 0.2261 0.22149 0.2497 RANDOM 27.819
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] -0.67 0.83 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.232 r_dihedral_angle_4_deg 14.516 r_dihedral_angle_3_deg 13.45 r_long_range_B_refined 7.99 r_long_range_B_other 7.756 r_dihedral_angle_1_deg 7.239 r_scangle_other 5.25 r_mcangle_other 3.396 r_mcangle_it 3.391 r_scbond_it 3.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.232 r_dihedral_angle_4_deg 14.516 r_dihedral_angle_3_deg 13.45 r_long_range_B_refined 7.99 r_long_range_B_other 7.756 r_dihedral_angle_1_deg 7.239 r_scangle_other 5.25 r_mcangle_other 3.396 r_mcangle_it 3.391 r_scbond_it 3.189 r_scbond_other 3.189 r_mcbond_other 2.23 r_mcbond_it 2.217 r_angle_refined_deg 1.528 r_angle_other_deg 1.347 r_chiral_restr 0.074 r_bond_refined_d 0.008 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 302 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction