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Crystal structure of the mutated tRNA-guanine transglycosylase (TGT) D280E complexed with preQ1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PUD PDB entry 1PUD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 PEG 8000, dimethylsulfoxide, tris hydrochloride, DTT, preQ1, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.16 49.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.28 α = 90 b = 64.94 β = 96.12 c = 70.2 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 103 IMAGE PLATE RIGAKU RAXIS IV osmic mirrors 2002-11-06 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 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 1.7 40 94.5 0.067 0.067 24.3 3.6 42492
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 90.6 0.253 0.253 6.1 3.7 42492
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 PDB entry 1PUD 1.7 10 41592 39504 2088 93 0.1607 0.1594 0.1594 0.1691 0.206 0.1798 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 8 2736.99 3169.49
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.064 s_non_zero_chiral_vol 0.053 s_zero_chiral_vol 0.047 s_angle_d 0.027 s_from_restr_planes 0.0234 s_anti_bump_dis_restr 0.017 s_bond_d 0.008 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2815 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 62
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement SCALEPACK data scaling SHELX phasing