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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 5.6 291 21-24% PEG 400, 0.1 M sodium citrate pH5.6, 10% isopropanol
Crystal Properties Matthews coefficient Solvent content 2.5 50.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.774 α = 90 b = 87.774 β = 90 c = 83.105 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 CCD RAYONIX MX300-HS 2018-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 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 1.95 76.28 98.6 0.061 14.2 5.3 52180
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 1.95 2 0.514
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 1.95 76.01 48724 2700 98.55 0.2298 0.2283 0.2352 0.2575 0.2637 RANDOM 47.018
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] -0.51 -0.26 -0.51 1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.757 r_dihedral_angle_4_deg 19.334 r_dihedral_angle_3_deg 12.985 r_dihedral_angle_1_deg 5.499 r_angle_refined_deg 1.142 r_angle_other_deg 0.89 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.757 r_dihedral_angle_4_deg 19.334 r_dihedral_angle_3_deg 12.985 r_dihedral_angle_1_deg 5.499 r_angle_refined_deg 1.142 r_angle_other_deg 0.89 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4903 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing PDB_EXTRACT data extraction