☰ Navigation Tabs
PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3Dpol in complex with Z57328552
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 2.45 49.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.473 α = 90 b = 83.479 β = 108.2 c = 59.046 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 0.92202 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 1.52 46.55 95.4 0.083 0.091 0.036 0.994 11.7 5.6 74844
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 1.52 1.55 63.6 1.369 1.814 1.17 0.571 2.3
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 1.52 46.6 70930 3789 95.13 0.2092 0.2075 0.2177 0.2418 0.2465 RANDOM 29.603
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] -1.94 0.72 2.19 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.262 r_dihedral_angle_4_deg 13.838 r_dihedral_angle_3_deg 13.468 r_dihedral_angle_1_deg 6.73 r_mcangle_it 3.091 r_mcbond_it 2.33 r_mcbond_other 2.32 r_angle_refined_deg 1.569 r_angle_other_deg 1.356 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.262 r_dihedral_angle_4_deg 13.838 r_dihedral_angle_3_deg 13.468 r_dihedral_angle_1_deg 6.73 r_mcangle_it 3.091 r_mcbond_it 2.33 r_mcbond_other 2.32 r_angle_refined_deg 1.569 r_angle_other_deg 1.356 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 332 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing