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Crystal structure of E. coli tRNA pseudouridine synthase TruD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 PEG 5000MME, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.18 α = 90 b = 108.11 β = 90 c = 112.52 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH 2003-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.93219 BESSY 14.1
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 79.06 99.9 0.072 15.9 52753 52753 -3 -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 2.1 100 0.36
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 35 -3 51156 51075 1678 99.84 0.19397 0.19397 0.19246 0.1998 0.23913 0.2402 RANDOM 15.257
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] 0.06 -0.08 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.512 r_scangle_it 3.762 r_scbond_it 2.457 r_angle_refined_deg 1.659 r_mcangle_it 1.467 r_angle_other_deg 0.912 r_mcbond_it 0.898 r_symmetry_vdw_other 0.323 r_nbd_other 0.249 r_symmetry_hbond_refined 0.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.512 r_scangle_it 3.762 r_scbond_it 2.457 r_angle_refined_deg 1.659 r_mcangle_it 1.467 r_angle_other_deg 0.912 r_mcbond_it 0.898 r_symmetry_vdw_other 0.323 r_nbd_other 0.249 r_symmetry_hbond_refined 0.212 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.199 r_symmetry_vdw_refined 0.107 r_chiral_restr 0.106 r_nbtor_other 0.088 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5252 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling SHELXD phasing