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Crystal structure of THF riboswitch, unbound status
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SUX pdb entry 3SUX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 0.1 M Tris-HCl, pH 7.0
4.2 M Na-formate, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 3.4 63.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.172 α = 90 b = 124.172 β = 90 c = 150.428 γ = 120
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 2011-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C APS 24-ID-C
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 3.2 30 99.7 0.103 26.1 6.7 7473 7451 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.31 99.6 0.74 2.1 6.9 738
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT pdb entry 3SUX 3.21 20 7105 7084 341 99.7 0.22499 0.22499 0.22281 0.2121 0.26906 0.2623 RANDOM 103.08
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] 1 0.5 1 -1.5
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 1.525 r_angle_refined_deg 1.361 r_scbond_it 0.795 r_nbtor_refined 0.276 r_xyhbond_nbd_refined 0.184 r_nbd_refined 0.162 r_symmetry_hbond_refined 0.148 r_symmetry_vdw_refined 0.146 r_chiral_restr 0.057 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 1.525 r_angle_refined_deg 1.361 r_scbond_it 0.795 r_nbtor_refined 0.276 r_xyhbond_nbd_refined 0.184 r_nbd_refined 0.162 r_symmetry_hbond_refined 0.148 r_symmetry_vdw_refined 0.146 r_chiral_restr 0.057 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it 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 2176 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose CBASS data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing