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Crystal structure of human METTL1 and WDR4 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CKK 3CKK for METTL1, chain D of 2VDU for WDR4 experimental model PDB 2VDU 3CKK for METTL1, chain D of 2VDU for WDR4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 2M (NH4)2SO4, 0.2M K Na Tartrate, 0.1 M Na3 citrate pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.39 63.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.407 α = 90 b = 194.574 β = 90 c = 86.346 γ = 90
Symmetry Space Group C 2 2 21
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 EIGER2 X 16M monochromatros 2020-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.09 47.87 99 0.308 0.377 0.214 5.1 4.6 19262 85.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.09 3.31 97.5 2.649 3.236 1.831 0.9 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3CKK for METTL1, chain D of 2VDU for WDR4 3.1 47.87 1.34 18972 966 97.67 0.224 0.2215 0.2334 0.2708 0.2731 75.05
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 3.6801 f_angle_d 0.4346 f_chiral_restr 0.0425 f_plane_restr 0.0024 f_bond_d 0.0019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4327 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 15
Software Software Software Name Purpose BUSTER refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing