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tRNA guanine transglycosylase TGT E235Q mutant in complex with BDI (2-BUTYL-5,6-DIHYDRO-1H-IMIDAZO[4,5-D]PYRIDAZINE-4,7-DIONE)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P0B PDB ENTRY 1P0B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 8% PEG 8000, 100mM MES pH 5.5, 1mM DTT, 10% DMSO, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.42 49.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.878 α = 90 b = 65.324 β = 96.65 c = 70.615 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++ 2006-12-13 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 1.63 50 92.5 0.031 0.031 33 3.6 47068
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-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 PDB ENTRY 1P0B 1.63 26.46 44520 92.5 0.1339 0.1318 0.1443 0.1935 0.1966 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 16 2744 3172.5
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.071 s_non_zero_chiral_vol 0.059 s_similar_adp_cmpnt 0.053 s_zero_chiral_vol 0.049 s_angle_d 0.027 s_from_restr_planes 0.025 s_anti_bump_dis_restr 0.025 s_bond_d 0.009 s_rigid_bond_adp_cmpnt 0.003 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2800 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 70
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing