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Co-crystal structures of CHIKV nsP3 macrodomain with pyrimidone fragments
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 291 21-24% PEG 400, 0.1 M sodium citrate pH5.6, 10% isopropanol
Crystal Properties Matthews coefficient Solvent content 2.52 51.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.013 α = 90 b = 88.013 β = 90 c = 83.552 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 EIGER X 16M 2018-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 76.23 99.2 0.069 13.8 5.7 67119
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.847 0.566
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6VUQ 1.8 56.37 62874 3323 98.63 0.2115 0.2096 0.2199 0.248 0.2566 RANDOM 41.955
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] -0.48 -0.24 -0.48 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.379 r_dihedral_angle_4_deg 21.803 r_dihedral_angle_3_deg 14.817 r_dihedral_angle_1_deg 6.492 r_angle_refined_deg 1.507 r_angle_other_deg 0.998 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.379 r_dihedral_angle_4_deg 21.803 r_dihedral_angle_3_deg 14.817 r_dihedral_angle_1_deg 6.492 r_angle_refined_deg 1.507 r_angle_other_deg 0.998 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4896 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 48
Software Software Software Name Purpose XDS data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction