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Crystal structure of monkeypox virus methyltransferase VP39 in complex with inhibitor TO507
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 2.34 47.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.936 α = 90 b = 84.133 β = 90 c = 154.25 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 44.19 87.19 0.1501 0.1642 0.06444 0.993 10.59 5.9 21106 36.71
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 76.65 1.12 1.24 0.5113 0.71 1.36 4.8
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 44.19 1.35 21077 1054 87.22 0.2207 0.2182 0.2186 0.2718 0.2721 random selection 40.29
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 12.4307 f_angle_d 0.5697 f_chiral_restr 0.0432 f_plane_restr 0.0054 f_bond_d 0.0039
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4549 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 76
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing Coot model building PHENIX refinement