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Crystal structure of the adenosylcobalamin riboswitch holo conformation in absence of ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GMA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 RNA buffer: 10 mM HEPES pH 7.5, 100 mM KCl, 10 mM MgCl2; Crystallization Buffer: Molecular Dimensions Morpheus screen: 0.1 M Buffer System 1, pH 6.5, 30% Precipitant Mix 1, 0.1 M Carboxylic acids
Crystal Properties Matthews coefficient Solvent content 3.63 66.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.124 α = 90 b = 243.844 β = 90 c = 84.554 γ = 90
Symmetry Space Group C 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 PIXEL DECTRIS PILATUS 6M 2019-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.60747 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 4.3 41.78 92 0.095 0.105 0.999 5.62 5.2 6528 256.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4.3 4.41 3.589 3.97 0.32299999999999995
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MOLECULAR REPLACEMENT FREE R-VALUE 4.3 41.78 1.34 6500 302 91.78 0.2644 0.2626 0.2634 0.2949 0.2937 312.9
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 16.0055 f_angle_d 0.7149 f_chiral_restr 0.0342 f_plane_restr 0.0041 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 3990 Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling XDS data reduction PHASER phasing