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Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 25% (w/v) PEG 3350, 0.1 M Hepes, pH 7.5 and 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2 38.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.686 α = 90 b = 97.19 β = 112.04 c = 84.478 γ = 90
Symmetry Space Group P 1 21 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 270r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97902 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.1 50 100 0.092 0.092 24 3.7 57374
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 2.1 2.14 100 0.375 0.375 5.38 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 SAD THROUGHOUT 2.1 50 54282 2896 99.59 0.15088 0.14803 0.1592 0.20396 0.2093 RANDOM 27.88
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] -1.33 0.05 -1.14 1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.446 r_dihedral_angle_3_deg 16.016 r_dihedral_angle_4_deg 15.372 r_long_range_B_refined 6.801 r_long_range_B_other 6.69 r_dihedral_angle_1_deg 5.896 r_scangle_other 5.168 r_scbond_it 3.399 r_scbond_other 3.399 r_mcangle_it 3.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.446 r_dihedral_angle_3_deg 16.016 r_dihedral_angle_4_deg 15.372 r_long_range_B_refined 6.801 r_long_range_B_other 6.69 r_dihedral_angle_1_deg 5.896 r_scangle_other 5.168 r_scbond_it 3.399 r_scbond_other 3.399 r_mcangle_it 3.239 r_mcangle_other 3.239 r_mcbond_it 2.216 r_mcbond_other 2.216 r_angle_refined_deg 1.871 r_angle_other_deg 0.869 r_chiral_restr 0.106 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7290 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 121
Software Software Software Name Purpose ADSC data collection PHENIX model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling