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Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DJ0 1DJ0 (apo TruA enzyme) and 1EHZ (phe tRNA) experimental model PDB 1EHZ 1DJ0 (apo TruA enzyme) and 1EHZ (phe tRNA)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 20% PEG 3350, 0.2 M K3 Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.17 61.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.033 α = 90 b = 149.292 β = 90 c = 291.991 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 ADSC QUANTUM 210 2004-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.0 ALS 8.3.1
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 3.9 50 93.3 0.213 4.86 2.8 24919 24919
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) 3.9 4.04 93 0.619 1.56 2.6 2453
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1DJ0 (apo TruA enzyme) and 1EHZ (phe tRNA) 3.9 50 23996 23996 1163 89.4 0.2982 0.2597 0.3503 0.3028 RANDOM
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] -42.99 3.382 39.608
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.28717 c_bond_d 0.010398
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8278 Nucleic Acid Atoms 5991 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHASER phasing CNS refinement DENZO data reduction SCALEPACK data scaling