☰ Navigation Tabs
tRNA-Guanine Transglycosylase cocrystallized with pyridyl-alkine-substituted lin-benzoguanine ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P0D pdb entyr 1P0D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 288 100 MM MES, 1MM DTT, 10% DMSO, 13% PEG8000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.29 46.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.794 α = 90 b = 64.771 β = 93 c = 71.348 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 RAYONIX MX-225 Rh-coated silicon with indirect water cooling 2010-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
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 1.59 30 99.4 0.035 26.06 3.3 51448 51448 14.54
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) 1 1.59 1.62 99.3 0.091 11.92 3.3 2576
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R pdb entyr 1P0D 1.59 30 50801 48267 2534 97.8 0.1638 0.1638 0.1631 0.1953 0.1807 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 11 2485 2860
RMS Deviations Key Refinement Restraint Deviation s_zero_chiral_vol 0.055 s_similar_adp_cmpnt 0.054 s_non_zero_chiral_vol 0.052 s_anti_bump_dis_restr 0.029 s_angle_d 0.026 s_from_restr_planes 0.0246 s_bond_d 0.009 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2558 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 30
Software Software Software Name Purpose SHELXL-97 refinement CNS refinement MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing