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Crystal structure of the human METTL3-METTL14 in complex with small molecule inhibitor Compound 8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7O2I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.2 M calcium chloride, 0.1 M Tris:HCl pH 8.0, 18% (w/v) PEG 4000, sitting drop, protein:precipitant solution ratio = 1:1
Crystal Properties Matthews coefficient Solvent content 2.49 50.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.068 α = 90 b = 64.068 β = 90 c = 225.217 γ = 120
Symmetry Space Group P 32 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 EIGER X 16M 2023-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9785 SOLEIL PROXIMA 1
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 1.85 45.04 100 0.99 11.7 12.9 44645
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 1.85 1.89 0.42
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 THROUGHOUT 1.85 44.66 44645 2316 99.97 0.19439 0.192 0.2013 0.23994 0.2449 RANDOM 33.155
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] 0.11 0.06 0.11 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.682 r_long_range_B_refined 9.062 r_long_range_B_other 9.025 r_dihedral_angle_2_deg 7.338 r_dihedral_angle_1_deg 7.223 r_scangle_other 6.091 r_mcangle_it 5.395 r_mcangle_other 5.394 r_scbond_it 3.804 r_scbond_other 3.803
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.682 r_long_range_B_refined 9.062 r_long_range_B_other 9.025 r_dihedral_angle_2_deg 7.338 r_dihedral_angle_1_deg 7.223 r_scangle_other 6.091 r_mcangle_it 5.395 r_mcangle_other 5.394 r_scbond_it 3.804 r_scbond_other 3.803 r_mcbond_it 3.502 r_mcbond_other 3.5 r_angle_refined_deg 1.407 r_angle_other_deg 0.454 r_chiral_restr 0.063 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3770 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing