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Trna-gunanine-transglycosylase (TGT) mutant Y106F, C158V, A232S, V233G- APO-Structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y5X PDB ENTRY 1Y5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 100 mM Tris/HCl, 1 mM DTT, 5% PEG 8000, 10% DMSO, pH 8.50
Crystal Properties Matthews coefficient Solvent content 2.39 48.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.73 α = 90 b = 64.83 β = 96.31 c = 70.81 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 IMAGE PLATE RIGAKU RAXIS IV 2004-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 1.6 50 98.6 0.1331 0.071 15 2.9 53101
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 MOLECULAR REPLACEMENT FREE R PDB ENTRY 1Y5X 1.6 28.42 51779 98.6 0.1644 0.162 0.1657 0.221 0.216 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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 3 2815 3240.5
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.077 s_similar_adp_cmpnt 0.053 s_non_zero_chiral_vol 0.046 s_zero_chiral_vol 0.044 s_angle_d 0.027 s_from_restr_planes 0.024 s_anti_bump_dis_restr 0.021 s_bond_d 0.009 s_rigid_bond_adp_cmpnt 0.002 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2771 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 13
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing