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Crystal structure of YbxF bound to the SAM-I riboswitch aptamer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SDS M. jannaschii L7Ae protein (PDB ID 1SDS, chain A)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294.15 150 M RNA, 210 M YbxF, 10 mM MgCl2, 10 mM SAM, 40 mM KCl, 20 mM HEPES-KOH, 1 mM spermine, 1 mM cobalt hexammine, and 1 mM DTT, 100 mM potassium cacodylate pH 6.0, 200 mM MgCl2 and 25% (v/v) PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K
Crystal Properties Matthews coefficient Solvent content 2.52 51.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 191.762 α = 90 b = 54.305 β = 116.56 c = 106.366 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 ADSC QUANTUM 315r 2011-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1 ALS 5.0.2
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 2.8 50 0.098 25.2 4.3 25202 22926 116.2 121.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 92.7 2.46 4.3 2244
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT M. jannaschii L7Ae protein (PDB ID 1SDS, chain A) 2.8 29.54 22926 2276 93.4 0.218 0.218 0.2208 0.274 0.2711 RANDOM 75.6
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] 25.12 15.88 7.19 -32.32
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.5 c_scangle_it 6.87 c_mcangle_it 5.58 c_scbond_it 4.99 c_mcbond_it 3.52 c_improper_angle_d 1.73 c_angle_deg 1.4 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.5 c_scangle_it 6.87 c_mcangle_it 5.58 c_scbond_it 4.99 c_mcbond_it 3.52 c_improper_angle_d 1.73 c_angle_deg 1.4 c_bond_d 0.006 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 962 Nucleic Acid Atoms 5372 Solvent Atoms 15 Heterogen Atoms 202
Software Software Software Name Purpose ALS data collection PHASER phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling