☰ Navigation Tabs
Trna-guanine transglycosylase (TGT) mutant in complex with 7-deaza-7-aminomethyl-guanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 100mM Tris/HCl, 1mM DTT, 5% PEG 8000, 10% DMSO, 14mg/ml TGT, 20mM preQ1, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.37 48.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.9 α = 90 b = 64.93 β = 96.36 c = 71.18 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 113 IMAGE PLATE RIGAKU RAXIS IV mirrors 2004-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.46 20 98.6 0.044 18 3.2 64991 64991
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-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 MOLECULAR REPLACEMENT FREE R 1Y5X 1.46 8 64991 64991 38064 92.3 0.1515 0.15 0.15 0.1567 0.1984 0.1719 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 31 2827 3365
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.084 s_zero_chiral_vol 0.072 s_non_zero_chiral_vol 0.067 s_similar_adp_cmpnt 0.051 s_anti_bump_dis_restr 0.034 s_angle_d 0.031 s_from_restr_planes 0.0284 s_bond_d 0.011 s_rigid_bond_adp_cmpnt 0.004 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2739 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 50
Software Software Software Name Purpose CrystalClear data collection CNS refinement SHELXL refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing