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The Crystal Structure of tRNA (5-Methylaminomethyl-2-Thiouridylate)-Methyltransferase TrmU from Streptococcus pneumoniae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 100mM Tris pH=8.5, and 3.5M NaFormate, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 4.64 73.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.319 α = 90 b = 93.319 β = 90 c = 157.018 γ = 120
Symmetry Space Group P 32 2 1
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 ADSC QUANTUM 315 mirrors 2006-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97912 APS 19-ID
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 2.41 44.73 98.7 0.127 11.8 7.2 32091 31670
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 2.41 2.5 88.7 0.578 2.78 4 2791
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 2.41 44.73 27925 27925 3118 99.42 0.19315 0.19315 0.19049 0.1843 0.21661 0.2058 RANDOM 63.346
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] 2.95 1.48 2.95 -4.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.887 r_dihedral_angle_4_deg 22.018 r_dihedral_angle_3_deg 19.196 r_dihedral_angle_1_deg 6.232 r_scangle_it 3.145 r_scbond_it 2.082 r_angle_refined_deg 1.498 r_mcangle_it 1.477 r_mcbond_it 0.852 r_nbd_refined 0.218
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.887 r_dihedral_angle_4_deg 22.018 r_dihedral_angle_3_deg 19.196 r_dihedral_angle_1_deg 6.232 r_scangle_it 3.145 r_scbond_it 2.082 r_angle_refined_deg 1.498 r_mcangle_it 1.477 r_mcbond_it 0.852 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.123 r_chiral_restr 0.113 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2867 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building