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Crystal structure of monkeypox virus methyltransferase VP39 in complex with inhibitor TO500
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8B07
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 200 mM lithium citrate,
14.5% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.32 47.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.606 α = 90 b = 84.055 β = 90 c = 154.054 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 PILATUS 6M 2023-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 2.5 48.93 91.12 0.1896 0.207 0.08119 0.99 8.47 6.2 22141 37.9
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 2.5 2.589 78.45 1.239 1.365 0.5534 0.558 1.27 5.5
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.5 48.93 1.34 21840 1094 91.14 0.238 0.2358 0.2383 0.2818 0.2832 random selection 41.05
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 12.8535 f_angle_d 0.6924 f_chiral_restr 0.0449 f_plane_restr 0.0063 f_bond_d 0.0046
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4548 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 74
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing Coot model building PHENIX refinement