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Free-state structural transitions of the SAM-I riboswitch
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GIS PDB entry 2GIS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 7 303 pH 7.0, hanging drop, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.5 50.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.98 α = 90 b = 61.98 β = 90 c = 159.07 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 IV++ 2007-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.7 20 99.8 0.073 12.4 3.74 16190 34.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.7 2.8 100 0.278 4.6 3.68
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 2GIS 2.7 20 16219 16027 1529 98.8 0.259 0.259 0.2387 0.299 0.2863 50.61
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] 10.68 10.68 -21.36
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.3 c_scangle_it 2.2 c_improper_angle_d 2.1 c_mcangle_it 1.8 c_angle_deg 1.4 c_scbond_it 1.38 c_mcbond_it 1.25 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.3 c_scangle_it 2.2 c_improper_angle_d 2.1 c_mcangle_it 1.8 c_angle_deg 1.4 c_scbond_it 1.38 c_mcbond_it 1.25 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 Nucleic Acid Atoms 2031 Solvent Atoms 33 Heterogen Atoms 38
Software Software Software Name Purpose d*TREK data scaling CNS refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction CNS phasing