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Crystal structure of THF riboswitch, bound with 5-formyl-THF
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 6.6 293.15 Na-Cacodylate, pH 6.6
3.2M M Na-formate, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 3.5 64.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.597 α = 90 b = 126.597 β = 90 c = 149.164 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 2011-06-11 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 2.65 30 100 0.058 32.5 5.5 13605 13605 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 2.65 2.74 100 0.553 5.6
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 2.65 30 12892 12889 670 99.97 0.21138 0.21138 0.20962 0.2049 0.24648 0.2465 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.145 r_nbtor_refined 0.287 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.165 r_symmetry_hbond_refined 0.149 r_gen_planes_refined 0.012 r_bond_refined_d 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.145 r_nbtor_refined 0.287 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.165 r_symmetry_hbond_refined 0.149 r_gen_planes_refined 0.012 r_bond_refined_d 0.006 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_chiral_restr 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_scbond_it r_scangle_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 21 Heterogen Atoms 36
Software Software Software Name Purpose CBASS data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing