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tRNA guanine transglycosylase E235Q mutant apo structure, pH 8.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OKO PDB ENTRY 2OKO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 5% PEG 8000, 100mM Tris/HCl pH 8.5, 1mM DTT, 10% DMSO, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.41 49.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.757 α = 90 b = 65.175 β = 96.12 c = 70.455 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++ 2006-07-12 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 1.55 20 95.6 0.058 0.058 16 2.3 56093
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 2OKO 1.55 20 53093 95.6 0.1443 0.1426 0.1481 0.2032 0.1995 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 7 2823 3205.5
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.072 s_zero_chiral_vol 0.053 s_non_zero_chiral_vol 0.053 s_similar_adp_cmpnt 0.051 s_anti_bump_dis_restr 0.029 s_angle_d 0.028 s_from_restr_planes 0.025 s_bond_d 0.01 s_rigid_bond_adp_cmpnt 0.003 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2859 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 25
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing