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tRNA-Guanine Transglycosylase in complex with N-Methyl-lin-Benzoguanine Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P0D pdb entry 1P0D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 288 100MM TRIS HCL, 1MM DTT, 10% DMSO,
5% PEG 8000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.2 48.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.671 α = 90 b = 64.754 β = 95.99 c = 70.457 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 2010-02-26 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 1.68 30 96.3 0.059 19.5 2.9 45107 45107 15.8
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 1.68 1.71 90.9 0.287 3.2 2.3 2115
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION AB INITIO PHASING FREE R pdb entry 1P0D 1.68 30 42831 40685 2146 92.5 0.1602 0.159 0.1628 0.2004 0.1732 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 2745.95 3119.54
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.049 s_zero_chiral_vol 0.043 s_non_zero_chiral_vol 0.043 s_angle_d 0.024 s_from_restr_planes 0.024 s_anti_bump_dis_restr 0.019 s_bond_d 0.007 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2799 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 31
Software Software Software Name Purpose SHELXL-97 refinement CNS refinement MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing