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METTL3-METTL14 heterodimer bound to the SAM competitive small molecule inhibitor STM2457
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5L6D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 150 mM magnesium acetate, 22% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.24 45.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.094 α = 90 b = 64.094 β = 90 c = 225.302 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 2019-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 3 49.795 100 0.274 0.996 12.2 19.7 11480
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.18 100 1.8 0.697 2.7 15
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5L6D 3 49.795 11432 508 99.956 0.189 0.1859 0.1944 0.2626 0.2759 60.364
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] -1.463 -0.731 -1.463 4.745
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.741 r_dihedral_angle_3_deg 19.605 r_dihedral_angle_4_deg 17.413 r_dihedral_angle_1_deg 8.673 r_lrange_it 8.17 r_lrange_other 8.169 r_mcangle_it 5.202 r_mcangle_other 5.202 r_scangle_it 4.99 r_scangle_other 4.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.741 r_dihedral_angle_3_deg 19.605 r_dihedral_angle_4_deg 17.413 r_dihedral_angle_1_deg 8.673 r_lrange_it 8.17 r_lrange_other 8.169 r_mcangle_it 5.202 r_mcangle_other 5.202 r_scangle_it 4.99 r_scangle_other 4.99 r_mcbond_it 3.117 r_mcbond_other 3.104 r_scbond_it 3.037 r_scbond_other 3.037 r_angle_refined_deg 1.287 r_angle_other_deg 1.135 r_nbd_refined 0.235 r_symmetry_nbd_other 0.225 r_nbd_other 0.216 r_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.178 r_symmetry_nbd_refined 0.115 r_symmetry_xyhbond_nbd_refined 0.113 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.058 r_chiral_restr 0.055 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3580 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing