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Crystal Structure of the N-terminal domain of human METTL16 in complex with SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H00
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 1.3 M K2HPO4, 45 mM NaH2PO4; drop contained 4 uL of protein solution (27 mg/mL) and 2 uL of reservoir solution; 0.2 uL of 200 mM SAM solution (buffered in 50 mM Hepes pH7.5) was added to the drop with mature crystals. 25% ethylene glycol was used for cryo-protection
Crystal Properties Matthews coefficient Solvent content 4.77 74.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 190.351 α = 90 b = 190.351 β = 90 c = 190.351 γ = 90
Symmetry Space Group I 41 3 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 CCD RAYONIX MX300-HS 2017-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.1 50 99.3 0.064 0.066 1 28.7 17.3 34224
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.23 95.9 1.36 1.41 0.72 2 14.2
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 (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 FREE R-VALUE 2h00 2.1 44.87 33194 1027 99.34 0.182 0.181 0.1875 0.219 0.2163 RANDOM 54.009
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 r_dihedral_angle_2_deg 36.476 r_dihedral_angle_4_deg 18.363 r_dihedral_angle_3_deg 15.232 r_long_range_B_refined 7.766 r_long_range_B_other 7.764 r_dihedral_angle_1_deg 6.458 r_scangle_other 4.606 r_mcangle_it 3.498 r_mcangle_other 3.496 r_scbond_other 2.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.476 r_dihedral_angle_4_deg 18.363 r_dihedral_angle_3_deg 15.232 r_long_range_B_refined 7.766 r_long_range_B_other 7.764 r_dihedral_angle_1_deg 6.458 r_scangle_other 4.606 r_mcangle_it 3.498 r_mcangle_other 3.496 r_scbond_other 2.842 r_scbond_it 2.84 r_mcbond_it 2.273 r_mcbond_other 2.258 r_angle_refined_deg 1.676 r_angle_other_deg 1.016 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2113 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing