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Crystal structure of archaeosine tRNA-guanine transglycosylase complexed with guanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IQ8 PDB ENTRY 1IQ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Na phosphate, K phosphate, Na acetate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.43 64.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.201 α = 90 b = 100.201 β = 90 c = 364.658 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS V mirrors 2001-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45PX 1.02 SPring-8 BL45PX
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 2.3 50 98.4 0.107 0.107 19.6 6.9 567949 567949 15
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) 2.3 2.34 96.7 0.382 0.382 3.78 4.6 3973
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1IQ8 2.3 50 82093 8228 98.3 0.229 0.229 0.271 RANDOM 35.7
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] 4.82 4.82 -9.65
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.6 c_scangle_it 3.04 c_mcangle_it 2.01 c_scbond_it 2.01 c_angle_deg 1.3 c_mcbond_it 1.23 c_improper_angle_d 0.87 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.6 c_scangle_it 3.04 c_mcangle_it 2.01 c_scbond_it 2.01 c_angle_deg 1.3 c_mcbond_it 1.23 c_improper_angle_d 0.87 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9304 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 15
Software Software Software Name Purpose AMoRE phasing CNS refinement DENZO data reduction SCALEPACK data scaling