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Crystal structure of the human METTL16 Methyltransferase Domain in complex with a bisubstrate analogue (BA4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B91
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 1.413 M K2HPO4, 0.045 M NaH2PO4, drops containing 4 microliter of protein (27 mg/mL) and 2 microliter reservoir solution. Mature crystals were soaked in a drop containing 50 mM BA4 in 1.43 M K2HPO4, 0.045 M NaH2PO4, 25 % Ethylene Glycol.
Crystal Properties Matthews coefficient Solvent content 4.2 70.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.783 α = 90 b = 188.783 β = 90 c = 188.783 γ = 90
Symmetry Space Group I 41 3 2
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 2026-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.169 77.07 100 0.173 0.174 0.019 0.999 26.4 81.7 30596
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.169 2.206 100 0.374
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 2.17 77.07 1.35 30587 1470 99.97 0.2088 0.2075 0.2085 0.2339 0.2355
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 17.876 f_angle_d 0.885 f_chiral_restr 0.053 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2030 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 79
Software Software Software Name Purpose PHENIX refinement autoPROC data scaling PHASER phasing PDB_EXTRACT data extraction autoPROC data reduction