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Crystal structure of YebU, a m5C RNA methyltransferase from E.coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 15%(w/v) PEG 8000, 50mM mono-potassium dihydrogen phosphate, 10mM BaCl2 or 15% PEG 5000 MME, sodium acetate pH 4.6, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.54 51.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.706 α = 88.33 b = 87.126 β = 76.79 c = 95.048 γ = 90.19
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 MAR CCD 165 mm Mirror followed by asymmetrically cut Si-111 monochromator 2003-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 0.962 MAX II I711
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 2.9 30 97.9 0.103 9.13 3.22 46876 45870 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 97.5 0.551 2.14 3.2 4493
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 2.9 29.03 46791 45743 2314 97.76 0.234 0.234 0.231 0.2158 0.282 0.2702 RANDOM 65.522
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] 0.07 0.01 0.04 0.03 -0.05 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.807 r_dihedral_angle_3_deg 22.484 r_dihedral_angle_4_deg 18.281 r_dihedral_angle_1_deg 7.613 r_scangle_it 2.524 r_angle_refined_deg 1.758 r_scbond_it 1.661 r_mcangle_it 0.798 r_mcbond_it 0.532 r_nbtor_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.807 r_dihedral_angle_3_deg 22.484 r_dihedral_angle_4_deg 18.281 r_dihedral_angle_1_deg 7.613 r_scangle_it 2.524 r_angle_refined_deg 1.758 r_scbond_it 1.661 r_mcangle_it 0.798 r_mcbond_it 0.532 r_nbtor_refined 0.326 r_nbd_refined 0.264 r_symmetry_hbond_refined 0.264 r_symmetry_vdw_refined 0.201 r_xyhbond_nbd_refined 0.196 r_chiral_restr 0.124 r_bond_refined_d 0.022 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14266 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling SHELXD phasing SOLVE phasing