☰ Navigation Tabs
Apo structure of the TPP riboswitch aptamer domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NYG The phasing was accomplished using MR-SAD, where modifications of 4NYG were used in conjunction with SAD data to generate initial phases.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M Tris-Bicine, pH 8.3,
12.5% MPD, 12.5% PEG 3350, 12.5% PEG 1000,
0.12 M ethylene glycol mixture
Crystal Properties Matthews coefficient Solvent content 2.56 51.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.264 α = 90 b = 139.264 β = 90 c = 97.905 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 PIXEL DECTRIS EIGER X 16M 2020-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.103025 APS 23-ID-B
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 3.1 48.95 99.9 0.115 0.122 0.041 0.999 17.6 14.9 19251 142.18
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 3.1 3.31 99.8 2.868 3.07 1.073 0.502 8.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 4NYG 3.1 45.58 1.33 18652 960 96.79 0.2836 0.2818 0.2965 0.3166 0.3357 143.14
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 f_dihedral_angle_d 21.1469 f_angle_d 1.0495 f_chiral_restr 0.0905 f_plane_restr 0.0041 f_bond_d 0.0035
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2922 Solvent Atoms Heterogen Atoms 229
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing