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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 2.47 50.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.03 α = 90 b = 87.03 β = 90 c = 83.845 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 PILATUS 200K 2019-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU R-AXIS IV 1.5418
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 2.2 75.38 99.7 0.07 17.4 1.9 35519
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 2.2 2.268 0.51
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 2.21 43.55 33717 1724 99.7 0.2153 0.2125 0.2189 0.2712 0.276 RANDOM 46.532
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] 0.08 0.04 0.08 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.35 r_dihedral_angle_4_deg 19.838 r_dihedral_angle_3_deg 15.217 r_dihedral_angle_1_deg 6.689 r_angle_refined_deg 1.395 r_angle_other_deg 1.252 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.35 r_dihedral_angle_4_deg 19.838 r_dihedral_angle_3_deg 15.217 r_dihedral_angle_1_deg 6.689 r_angle_refined_deg 1.395 r_angle_other_deg 1.252 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4918 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction