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Z. mobilis tRNA guanine transglycosylase E235Q mutant apo-structure at pH 5.5
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 5.5 pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.33 49.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.407 α = 90 b = 65.194 β = 96.36 c = 70.514 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 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 1.5 50 91.5 0.1224 0.032 33 3.5 210241
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 1Y5X 1.5 10 210241 210241 85.9 0.1256 0.1256 0.1254 0.1353 0.1739 0.1774 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 19 2810 3355.5
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.081 s_anti_bump_dis_restr 0.065 s_zero_chiral_vol 0.063 s_non_zero_chiral_vol 0.062 s_similar_adp_cmpnt 0.054 s_angle_d 0.03 s_from_restr_planes 0.026 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 2823 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 97
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing