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Crystal structure of METTL9 in complex with compound 15k
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YF2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 291 0.1 M BICINE pH 9.0, 2% 1,4-Dioxane, 12% w/v PEG 20000, 12% Glycerol, 0.01 M TCEP
Crystal Properties Matthews coefficient Solvent content 2.34 47.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.394 α = 90 b = 45.651 β = 123.23 c = 106.895 γ = 90
Symmetry Space Group C 1 2 1
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 PILATUS3 6M 2024-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97923 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.28 70.5 99.4 0.998 11.6 3.2 26532 37.02
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 2.28 2.4 99.9 0.895
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 2.28 35.57 1.35 26501 2000 99.2 0.2235 0.2193 0.221 0.273 0.2753 44.97
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 11.0159 f_angle_d 0.4613 f_chiral_restr 0.0385 f_plane_restr 0.0034 f_bond_d 0.0023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4018 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 72
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing