☰ Navigation Tabs
PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3Dpol in complex with Z190780124
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XE0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 0.1 M TRIS-HCl (pH 8.5), 16% PEG 3350, 16% Isopropanol
Crystal Properties Matthews coefficient Solvent content 2.42 49.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.377 α = 90 b = 82.784 β = 108.47 c = 58.967 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 XE 9M 2024-11-15 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92203 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 55.91 90.6 0.117 0.128 0.05 0.996 8.2 6.2 63634
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 47.1 2.584 2.942 1.385 0.367 4.4
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 FOURIER SYNTHESIS THROUGHOUT 1.57 55.93 58462 3111 87.71 0.2124 0.2104 0.2194 0.2493 0.2512 RANDOM 29.884
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] -0.69 0.64 2.28 -1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.562 r_dihedral_angle_4_deg 16.623 r_dihedral_angle_3_deg 14.348 r_dihedral_angle_1_deg 6.913 r_mcangle_it 3.045 r_mcbond_it 2.185 r_mcbond_other 2.178 r_angle_refined_deg 1.477 r_angle_other_deg 1.298 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.562 r_dihedral_angle_4_deg 16.623 r_dihedral_angle_3_deg 14.348 r_dihedral_angle_1_deg 6.913 r_mcangle_it 3.045 r_mcbond_it 2.185 r_mcbond_other 2.178 r_angle_refined_deg 1.477 r_angle_other_deg 1.298 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3639 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing