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Structure of 5'-deoxy-5'-methylthioadenosine phosphorylase homologue from Sulfolobus tokodaii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CG6 PDB code 1cg6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 Tris buffer, PEG1000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.64 53.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.869 α = 90 b = 142.888 β = 90 c = 169.564 γ = 90
Symmetry Space Group C 2 2 21
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 ADSC QUANTUM 4 a mirror and monochrometer 2003-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 1.0000 Photon Factory BL-18B
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 2.45 50 100 0.101 13.7 6.93 36084 36084 -3 33.59
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) 2.45 2.54 100 0.229 0.229 6.81 3576
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB code 1cg6 2.45 50 36061 36061 1806 100 0.1903 0.1911 0.2409 0.2415 RANDOM 34.228
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] -8.066 -2.035 10.101
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.49259 c_scangle_it 3.041 c_mcangle_it 2.34 c_scbond_it 2.14 c_angle_deg 2.12317 c_mcbond_it 1.4 c_improper_angle_d 1.33247 c_bond_d 0.021457
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6264 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement