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Crystal structure of Queuine tRNA-ribosyltransferase (EC 2.4.2.29) (tRNA-guanine (tm1561) from THERMOTOGA MARITIMA at 1.90 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EFZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 10 293 15.0% PEG-8000, 0.2M NaCl, 0.1M CHES pH 10.0 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.62 52.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.467 α = 90 b = 99.422 β = 123.8 c = 124.163 γ = 90
Symmetry Space Group C 1 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 210 2004-03-10 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 210 KOHZU: double crystal Si(111) 2004-02-05 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0000 ALS 8.2.1 2 SYNCHROTRON ALS BEAMLINE 8.3.1 1.115902, 1.282804 ALS 8.3.1
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 1.9 51.7 99.4 0.059 0.059 6.6 3.4 133817
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 1.9 1.95 99.8 0.659 0.659 0.4 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD, MOLECULAR REPLACEMENT THROUGHOUT 1EFZ 1.9 51.7 124830 6626 96.9 0.195 0.193 0.1961 0.229 0.229 RANDOM 22.259
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] -0.89 -0.04 0.49 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.766 r_dihedral_angle_4_deg 16.007 r_dihedral_angle_3_deg 13.827 r_dihedral_angle_1_deg 6.195 r_scangle_it 3.696 r_scbond_it 2.458 r_angle_refined_deg 1.583 r_mcangle_it 1.475 r_angle_other_deg 1.009 r_mcbond_it 0.989
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.766 r_dihedral_angle_4_deg 16.007 r_dihedral_angle_3_deg 13.827 r_dihedral_angle_1_deg 6.195 r_scangle_it 3.696 r_scbond_it 2.458 r_angle_refined_deg 1.583 r_mcangle_it 1.475 r_angle_other_deg 1.009 r_mcbond_it 0.989 r_symmetry_vdw_other 0.329 r_symmetry_vdw_refined 0.297 r_symmetry_hbond_refined 0.242 r_mcbond_other 0.238 r_nbd_refined 0.208 r_nbd_other 0.199 r_nbtor_refined 0.183 r_metal_ion_refined 0.161 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.094 r_nbtor_other 0.09 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_xyhbond_nbd_other 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11070 Nucleic Acid Atoms Solvent Atoms 655 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling SHELXD phasing autoSHARP phasing MOLREP phasing