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METTL3-METTL14 heterodimer bound to the SAM competitive small molecule inhibitor STM3006
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5L6D 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 = 63.97 α = 90 b = 63.97 β = 90 c = 226.48 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 2020-04-22 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) 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 2.213 75.493 100 0.999 12 9.9 27798
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 2.213 2.252 0.611 1.6
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 2.213 75.493 27797 1377 99.91 0.187 0.1842 0.1925 0.2442 0.2455 47.357
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] -0.126 -0.063 -0.126 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.215 r_dihedral_angle_4_deg 19.636 r_dihedral_angle_3_deg 16.766 r_dihedral_angle_1_deg 8.2 r_lrange_other 7.901 r_lrange_it 7.899 r_scangle_it 5.613 r_scangle_other 5.612 r_mcangle_other 4.837 r_mcangle_it 4.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.215 r_dihedral_angle_4_deg 19.636 r_dihedral_angle_3_deg 16.766 r_dihedral_angle_1_deg 8.2 r_lrange_other 7.901 r_lrange_it 7.899 r_scangle_it 5.613 r_scangle_other 5.612 r_mcangle_other 4.837 r_mcangle_it 4.835 r_scbond_it 3.609 r_scbond_other 3.608 r_mcbond_it 3.154 r_mcbond_other 3.149 r_angle_refined_deg 1.945 r_angle_other_deg 1.356 r_nbd_refined 0.218 r_symmetry_nbd_other 0.195 r_nbd_other 0.179 r_nbtor_refined 0.176 r_symmetry_nbd_refined 0.174 r_xyhbond_nbd_refined 0.149 r_symmetry_xyhbond_nbd_other 0.121 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.081 r_symmetry_xyhbond_nbd_refined 0.077 r_bond_refined_d 0.013 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 3608 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing