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PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with Z2301685688
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 2.44 49.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.643 α = 90 b = 62.644 β = 90 c = 146.84 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 1.43 62.67 99.8 0.113 0.118 0.033 0.995 8.3 12.4 73983
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 1.43 1.45 96.9 2.509 2.666 0.884 0.323 8.9
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 1.43 57.69 67120 2999 94.76 0.20172 0.20081 0.2128 0.2196 0.2312 RANDOM 24.209
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] 0.14 1.02 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.489 r_dihedral_angle_4_deg 16.769 r_dihedral_angle_3_deg 13.061 r_dihedral_angle_1_deg 7.24 r_long_range_B_refined 6.214 r_long_range_B_other 6.128 r_scangle_other 4.607 r_mcangle_other 3.001 r_mcangle_it 2.998 r_scbond_it 2.853
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.489 r_dihedral_angle_4_deg 16.769 r_dihedral_angle_3_deg 13.061 r_dihedral_angle_1_deg 7.24 r_long_range_B_refined 6.214 r_long_range_B_other 6.128 r_scangle_other 4.607 r_mcangle_other 3.001 r_mcangle_it 2.998 r_scbond_it 2.853 r_scbond_other 2.852 r_mcbond_it 1.944 r_mcbond_other 1.932 r_angle_refined_deg 1.547 r_angle_other_deg 1.388 r_chiral_restr 0.076 r_bond_refined_d 0.009 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 311 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction