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Crystal structure of human m1A58 methyltransferase in a complex with tRNA3Lys and SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PWY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289.15 1microliter protein solution (4.8 mg/ml protein, 66.4 micromolar tRNA3Lys, 2 mM s-adenosyl-L-homocysteine, 1mM MgCl2 and 50 mM Hepes pH7.5) and 1 microliter reservoir solution (0.1 M NaAcetate, pH 4.8-5.0, 2% w/v PEG 4000, 15% v/v MPD) suspended 1000 microliters reservoir solution
Crystal Properties Matthews coefficient Solvent content 3.71 66.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.18 α = 90 b = 137.18 β = 90 c = 177.02 γ = 90
Symmetry Space Group P 43 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 103.15 CCD ADSC QUANTUM 315r 2014-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11587 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 97 99.9 0.078 18.6 8.1 113960 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.5 99.9 2.23 1 7.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2PWY 2 74.373 1.34 113874 5683 99.94 0.2 0.1988 0.2029 0.2216 0.2261 random selection
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 14.715 f_angle_d 0.855 f_chiral_restr 0.046 f_bond_d 0.005 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5088 Nucleic Acid Atoms 1642 Solvent Atoms 416 Heterogen Atoms 27
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling