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Structure of Y. lipolytica Trm9-Trm112 complex, a methyltransferase modifying U34 in the anticodon loop of some tRNAs
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 100MM TRI-SODIUM CITRATE, 20%
POLYETHYLENE GLYCOL 4000 (PEG4K), 20% 2-PROPANOL, PH 7.5, VAPOR
DIFFUSION, SITTING DROP, TEMPERATURE 291K
Crystal Properties Matthews coefficient Solvent content 2.98 58.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.2 α = 90 b = 176.2 β = 90 c = 176.2 γ = 90
Symmetry Space Group I 4 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 PIXEL PSI PILATUS 6M 2012-05-11 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL PSI PILATUS 6M 2012-05-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9801 SOLEIL PROXIMA 1 2 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 1.2819, 1.2826, 1.2753 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.494 50 97.9 0.069 14.2 4.85 16239 52.14
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.65 98.3 0.501 0.501 2.5 4.85
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD FREE R-VALUE 2.5 44.05 2 16234 812 97.9 0.201 0.199 0.2094 0.242 0.2541 Random selection 57.7
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 15.355 f_angle_d 1.193 f_chiral_restr 0.05 f_bond_d 0.009 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2462 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling SHARP phasing XSCALE data scaling