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PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with Z1509711879
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 50.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.834 α = 90 b = 62.708 β = 90 c = 147.514 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 62.68 99.9 0.134 0.139 0.039 0.995 8.8 12.3 77624
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 97.2 2.821 3 1.003 0.27 8.5
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 1.41 57.78 72408 3016 97.15 0.19636 0.19577 0.2038 0.208 0.2148 RANDOM 22.717
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] 0.07 0.22 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.124 r_dihedral_angle_4_deg 13.659 r_dihedral_angle_3_deg 13.551 r_dihedral_angle_1_deg 7.455 r_long_range_B_refined 7.319 r_long_range_B_other 7.28 r_scangle_other 5.252 r_mcangle_other 3.376 r_mcangle_it 3.372 r_scbond_it 3.282
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.124 r_dihedral_angle_4_deg 13.659 r_dihedral_angle_3_deg 13.551 r_dihedral_angle_1_deg 7.455 r_long_range_B_refined 7.319 r_long_range_B_other 7.28 r_scangle_other 5.252 r_mcangle_other 3.376 r_mcangle_it 3.372 r_scbond_it 3.282 r_scbond_other 3.281 r_mcbond_it 2.251 r_mcbond_other 2.237 r_angle_refined_deg 1.685 r_angle_other_deg 1.397 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 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 312 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction