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Crystal structure of macrodomain from Eastern Equine Encephalitis Virus in complex with Adenosine diphosphate ribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9ZRC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 Bis-Tris pH 5.5, PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.82 32.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.925 α = 90 b = 47.462 β = 90 c = 66.421 γ = 90
Symmetry Space Group P 21 21 21
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 1.69 50 92.9 0.093 0.101 0.038 0.99 8.9 7 13670
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 1.7 1.73 61.4 0.446 0.519 0.255 0.857 3
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 1.69 38.62 1.38 12327 600 84.28 0.1746 0.1723 0.1726 0.2176 0.218
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 13.5 f_angle_d 0.776 f_chiral_restr 0.057 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1201 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 phasing