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Crystal structure of CHIKV nsp3 macrodomain with MDOLL-0273
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VUQ Nonstructural polyprotein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293.15 100 mM Tris, pH 8.0; 15 %w/v Polyvinylpyrrolidone K15; 25 %w/v Polyethylene glycol monomethyl ether 5,000
Crystal Properties Matthews coefficient Solvent content 2.64 53.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.9 α = 90 b = 86.9 β = 90 c = 84.96 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 16M 2025-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.953731 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.65 50 99.9 0.056 0.059 1 21.13 10.6 86300
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.69 99.9 0.99 1.05 0.748 2.16 10.56
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.65 43.488 86300 4315 99.887 0.147 0.1444 0.1524 0.1878 0.1897 34.382
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] 0.192 0.096 0.192 -0.623
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.376 r_dihedral_angle_4_deg 18.189 r_dihedral_angle_3_deg 13.356 r_dihedral_angle_1_deg 6.18 r_lrange_it 5.777 r_lrange_other 5.724 r_scangle_it 5.035 r_scangle_other 5.035 r_scbond_it 4.129 r_scbond_other 4.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.376 r_dihedral_angle_4_deg 18.189 r_dihedral_angle_3_deg 13.356 r_dihedral_angle_1_deg 6.18 r_lrange_it 5.777 r_lrange_other 5.724 r_scangle_it 5.035 r_scangle_other 5.035 r_scbond_it 4.129 r_scbond_other 4.128 r_mcangle_it 3.965 r_mcangle_other 3.965 r_mcbond_other 3.176 r_mcbond_it 3.175 r_rigid_bond_restr 1.674 r_angle_other_deg 1.323 r_angle_refined_deg 1.277 r_nbd_refined 0.201 r_nbd_other 0.18 r_symmetry_nbd_other 0.168 r_nbtor_refined 0.157 r_symmetry_xyhbond_nbd_refined 0.138 r_xyhbond_nbd_refined 0.132 r_symmetry_nbd_refined 0.132 r_ncsr_local_group_2 0.092 r_ncsr_local_group_6 0.089 r_ncsr_local_group_3 0.086 r_ncsr_local_group_4 0.078 r_ncsr_local_group_5 0.078 r_ncsr_local_group_1 0.076 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4949 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building