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Structure of the U65C mutant A-riboswitch aptamer from the Bacillus subtilis pbuE operon
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y26 PDB id 1Y26
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 296 2 mM Spermine, 50 mM Na Cacodylate, 32% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.42 49.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.93 α = 90 b = 46.33 β = 120.04 c = 87.24 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 315 2009-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.91924 NSLS X29A
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 2.8 26.04 99.1 0.13 10.5 3.6 10839 31.7
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) 2.8 2.93 99 0.63 3.1 3
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 id 1Y26 2.8 26.039 2 10839 1083 99.51 0.232 0.227 0.2228 0.277 0.269 30.376
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] -0.052 8.326 -10.795 10.847
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.321 f_angle_d 1.147 f_chiral_restr 0.052 f_bond_d 0.003 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2932 Solvent Atoms 88 Heterogen Atoms 11
Software Software Software Name Purpose CBASS data collection PHASER phasing PHENIX refinement XDS data reduction XSCALE data scaling