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Crystal structure of Pepper RNA aptamer in complex with HBC ligand and Fab BL3-6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KZD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 0.02 M Magnesium sulfate hydrate
0.002 M Cobalt(II) chloride hexahydrate
0.05 M Sodium cacodylate trihydrate pH 6.0
25% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.0005 M Spermine
Crystal Properties Matthews coefficient Solvent content 3.16 61.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.609 α = 90 b = 96.992 β = 90 c = 148.255 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER X 16M 2021-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979180 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.239 148.255 99.9 0.999 17.9 6.8 43646 62.32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.24 2.31 99.2 1.449 0.593 0.605 1.1 6.9
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 MOLECULAR REPLACEMENT FREE R-VALUE 4KZD 2.24 58.9 1.34 43546 1999 99.8 0.2213 0.2194 0.2193 0.2626 0.2588 69.89
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 14.3669 f_angle_d 0.5815 f_chiral_restr 0.0375 f_plane_restr 0.0034 f_bond_d 0.0025
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3303 Nucleic Acid Atoms 1407 Solvent Atoms 546 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement Coot model building MOSFLM data reduction SCALEPACK data scaling PHASER phasing