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METTL3/14 complex with switchable fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IL1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 10% w/v PEG 4000, 20% v/v
glycerol, 0.1 M bicine/Trizma
base pH, 8.5
0.02 M 1,6-hexanediol, 0.02 M 1-butanol, 0.02 M (RS)-1,2- propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3-propanediol
Crystal Properties Matthews coefficient Solvent content 2.3 46.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.83 α = 90 b = 100.83 β = 90 c = 117.7 γ = 90
Symmetry Space Group P 41 21 2
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 9M 2019-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 2.21 76.57 100 0.999 14.7 13 31097
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 2.21 2.27 100 0.606 13.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.21 76.57 31037 1544 99.958 0.177 0.1739 0.1835 0.2271 0.1912 61.864
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] 0.824 0.824 -1.647
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.115 r_dihedral_angle_6_deg 15.38 r_lrange_other 11.426 r_lrange_it 11.411 r_dihedral_angle_2_deg 10.371 r_scangle_it 9.241 r_scangle_other 9.239 r_dihedral_angle_1_deg 8.313 r_mcangle_it 6.979 r_mcangle_other 6.977
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.115 r_dihedral_angle_6_deg 15.38 r_lrange_other 11.426 r_lrange_it 11.411 r_dihedral_angle_2_deg 10.371 r_scangle_it 9.241 r_scangle_other 9.239 r_dihedral_angle_1_deg 8.313 r_mcangle_it 6.979 r_mcangle_other 6.977 r_scbond_it 6.905 r_scbond_other 6.904 r_mcbond_it 5.186 r_mcbond_other 5.16 r_angle_refined_deg 2.594 r_angle_other_deg 0.879 r_nbd_refined 0.219 r_symmetry_nbd_other 0.21 r_nbtor_refined 0.189 r_xyhbond_nbd_refined 0.177 r_symmetry_nbd_refined 0.171 r_nbd_other 0.165 r_symmetry_xyhbond_nbd_refined 0.157 r_chiral_restr 0.126 r_symmetry_nbtor_other 0.094 r_symmetry_xyhbond_nbd_other 0.089 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3957 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing