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Structure of the B. subtilis cobalamin riboswitch
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 287 Purified RNA was incubated at room temperature for 30 minutes in 25 mM Tris-HCl, pH 8.0, 50 mM potassium chloride, 10 mM magnesium chloride, 0.5 mM adenosylcobalamin prior to crystallization in 50 mM sodium cacodylate, 15% (v/v) PEG 400, 0.2 mM cobalt hexamine, 80 mM magnesium acetate, 1 mM spermine between pH 6.0 to pH 6.5 at 14C by vapor diffusion in a hanging drop format
Crystal Properties Matthews coefficient Solvent content 5.51 77.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.282 α = 90 b = 118.282 β = 90 c = 261.547 γ = 120
Symmetry Space Group P 65 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 RAYONIX MX-225 Mirrors 2013-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 3.253 39.213 92.8 0.16 0.162 0.025 0.996 18.2 47 15338
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.28 3.46 43.8 4.129 4.168 0.561 0.598 54
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MIRAS FREE R-VALUE 3.25 39.21 15338 785 86.3 0.263 0.2611 0.279 0.2741 129.1
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] 0.693 0.347 0.693 -2.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.013 r_scangle_other 3.118 r_scangle_it 3.117 r_angle_other_deg 2.165 r_scbond_it 1.847 r_scbond_other 1.847 r_dihedral_angle_3_deg 1.736 r_angle_refined_deg 0.807 r_nbtor_refined 0.253 r_nbd_other 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.013 r_scangle_other 3.118 r_scangle_it 3.117 r_angle_other_deg 2.165 r_scbond_it 1.847 r_scbond_other 1.847 r_dihedral_angle_3_deg 1.736 r_angle_refined_deg 0.807 r_nbtor_refined 0.253 r_nbd_other 0.22 r_xyhbond_nbd_refined 0.208 r_nbd_refined 0.148 r_chiral_restr 0.074 r_gen_planes_refined 0.033 r_gen_planes_other 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 3174 Solvent Atoms 48 Heterogen Atoms 179
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling SHARP phasing Coot model building