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Crystal structure of macrodomain from Chikungunya virus in complex with Adenosine diphosphate ribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9ZRA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 Sodium citrate
PEG 4000
Isopropanol
Crystal Properties Matthews coefficient Solvent content 2.6 52.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.535 α = 90 b = 87.535 β = 90 c = 82.53 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 2024-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97934 NSLS-II 17-ID-2
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 1.79 50 99.5 0.083 0.091 0.035 0.993 8.6 6.6 65754
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 1.8 1.83 98.7 0.71 0.787 0.331 0.619 5.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.79 38.67 1.98 62303 3089 94.13 0.1537 0.1517 0.1532 0.1924 0.194
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.741 f_angle_d 0.799 f_chiral_restr 0.054 f_plane_restr 0.007 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4911 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms 182
Software Software Software Name Purpose PHENIX refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 phasing