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Crystal structure of the human METTL3-METTL14 in complex with small molecule inhibitor Compound 4 / EP102
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 2.48 50.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.189 α = 90 b = 64.189 β = 90 c = 225.252 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 2023-08-03 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) R Merge I (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 1.75 49.9 100 0.14 1 16.1 20 52751
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 1.75 1.78 0.59
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 1.75 49.9 52751 2767 99.98 0.20397 0.2018 0.2132 0.24499 0.2518 RANDOM 37.684
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.228 r_long_range_B_refined 9.062 r_long_range_B_other 9.062 r_dihedral_angle_1_deg 7.44 r_dihedral_angle_2_deg 7.178 r_scangle_other 6.498 r_mcangle_it 6.018 r_mcangle_other 6.018 r_scbond_it 4.244 r_scbond_other 4.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.228 r_long_range_B_refined 9.062 r_long_range_B_other 9.062 r_dihedral_angle_1_deg 7.44 r_dihedral_angle_2_deg 7.178 r_scangle_other 6.498 r_mcangle_it 6.018 r_mcangle_other 6.018 r_scbond_it 4.244 r_scbond_other 4.243 r_mcbond_it 3.961 r_mcbond_other 3.951 r_angle_refined_deg 1.58 r_angle_other_deg 0.523 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 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 3802 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing