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METTL1 bound to the SAM competitive small molecule inhibitor STM9005
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other In-house MR model, originally derived from PDB 3CKK experimental model PDB 3CKK Used for original MR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 295 100 mM Bis-Tris pH 5.5, 200 mM LiSO4 and 20 % w/v PEG 3350, 10 mM STM5451
Crystal Properties Matthews coefficient Solvent content 2.63 53.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.986 α = 90 b = 85.986 β = 90 c = 66.69 γ = 120
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 S 9M 2022-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.437 74.466 95.7 0.0812 0.0833 0.0182 0.999 20.26 20.82 45010
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.437 1.509 63.7 2.3268 2.3952 0.5661 0.638 1.34 17.83 2250
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 (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 THROUGHOUT 1.437 20.65 44991 2313 88.2 0.1633 0.1619 0.1661 0.1909 0.187 RANDOM 27.82
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] -0.0201 -0.0201 0.0402
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 12.93 t_omega_torsion 4 t_angle_deg 1.01 t_bond_d 0.01 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1739 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 58
Software Software Software Name Purpose autoPROC data processing XDS data reduction pointless data scaling Aimless data scaling STARANISO data scaling MOLREP phasing Coot model building BUSTER refinement