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Crystal structure of the E. coli thiM riboswitch in complex with thieno[2,3-b]pyrazin-7-amine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HOJ PDB ENTRY 2HOJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 30% PEG2000, 0.5 M ammonium chloride, 50 mM Bis-Tris-HCl, pH 6.5, 10 mM manganese chloride, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.32 47.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.122 α = 90 b = 65.122 β = 90 c = 101.975 γ = 120
Symmetry Space Group P 32 1 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 CCD ADSC QUANTUM 315r 2012-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97741 ALS 5.0.1
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 3.15 30 100 0.111 8 10.7 4467
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 3.15 3.2 100 10.9 219
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2HOJ 3.15 30 4193 438 94.4 0.2019 0.2001 0.2639 0.2684 99.516
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] 13.798 13.798 -27.595
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.831 c_scbond_it 1.698 c_angle_d 1.194 c_bond_d 0.006 c_mcbond_it c_mcangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1647 Solvent Atoms 5 Heterogen Atoms 26
Software Software Software Name Purpose SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction PHASER phasing