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Structure of the M-Box Riboswitch Aptamer Domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 HEPES, MPD, Spermine, KCl, MgCl2 over 35 % MPD, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K 2 VAPOR DIFFUSION, HANGING DROP 7.2 293 HEPES, MPD, Spermine, CsCl, MgCl2 over 35 % MPD, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.655 α = 90 b = 101.081 β = 90 c = 285.765 γ = 90
Symmetry Space Group I 2 2 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 315 2006-04-17 M SINGLE WAVELENGTH 2 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV osmic mirrors 2006-06-17 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9786 APS 19-ID 2 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.6 50 99.3 0.107 0.107 6.8 4.4 22584 22584 59.6
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) 1,2 2.6 2.69 98.7 0.405 0.401 3 4.5 2202
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SIRAS THROUGHOUT 2.6 47.67 22181 22181 1131 99.37 0.204 0.204 0.202 0.1982 0.246 0.239 RANDOM 39.551
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] -3.83 -1.64 5.47
RMS Deviations Key Refinement Restraint Deviation r_mcbond_it 1.8 r_angle_refined_deg 1.73 r_scangle_it 1.603 r_scbond_it 1.126 r_symmetry_hbond_refined 0.332 r_nbtor_refined 0.279 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.17 r_metal_ion_refined 0.088
RMS Deviations Key Refinement Restraint Deviation r_mcbond_it 1.8 r_angle_refined_deg 1.73 r_scangle_it 1.603 r_scbond_it 1.126 r_symmetry_hbond_refined 0.332 r_nbtor_refined 0.279 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.17 r_metal_ion_refined 0.088 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 3263 Solvent Atoms 135 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-2000 data reduction HKL-2000 data scaling