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Group deposition for combi-soaks of Chikungunya virus nsP3 macrodomain -- Crystal structure of Chikungunya virus nsP3 macrodomain in complex with Z1741976468, Z3219959731 and Z4628744292 (CHIKV_MacB-x1689)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VUQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 293.15 0.1 M Potassium thiocyanate, 0.1 M Sodium bromide, 0.1 M Tris, pH 7.8, 25 % PEG Smear Broad
Crystal Properties Matthews coefficient Solvent content 2.64 53.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.282 α = 90 b = 87.282 β = 90 c = 85.574 γ = 120
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 2024-05-02 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92208 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 1.46 38.88 100 0.078 0.082 0.025 0.999 12.6 10 126744
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 1.46 1.48 99.8 2.576 2.773 1.009 0.335 7.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.46 38.91 116738 6129 96.91 0.19121 0.18952 0.22392 0.2365 RANDOM 29.957
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] 0.28 0.14 0.28 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.924 r_dihedral_angle_4_deg 19.729 r_dihedral_angle_3_deg 15.879 r_long_range_B_refined 6.913 r_long_range_B_other 6.593 r_dihedral_angle_1_deg 6.448 r_scangle_other 4.12 r_mcangle_it 2.593 r_mcangle_other 2.593 r_scbond_it 2.259
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.924 r_dihedral_angle_4_deg 19.729 r_dihedral_angle_3_deg 15.879 r_long_range_B_refined 6.913 r_long_range_B_other 6.593 r_dihedral_angle_1_deg 6.448 r_scangle_other 4.12 r_mcangle_it 2.593 r_mcangle_other 2.593 r_scbond_it 2.259 r_scbond_other 2.259 r_mcbond_other 1.475 r_angle_refined_deg 1.442 r_mcbond_it 1.385 r_angle_other_deg 1.292 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 4962 Nucleic Acid Atoms Solvent Atoms 586 Heterogen Atoms 178
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction