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Crystal structure of DasR in complex with a synthetic DasR-binding RNA aptamer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZS8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292.15 0.15 M potassium bromide, 30% w/v polyethylene glycol monomethyl ether 2,000, 30% v/v ethylene glycol.
(Hampton Research Index Screen solution 96 + Hampton Research Additive Screen solution 61; ratio 10:1)
Crystal Properties Matthews coefficient Solvent content 2.89 57.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.938 α = 90 b = 51.327 β = 108.735 c = 116.4 γ = 90
Symmetry Space Group P 1 21 1
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 2023-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.97625 PETRA III, EMBL c/o DESY P14 (MX2)
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 2.02 42.32 54.3 0.088 0.095 0.036 0.997 11.1 6.85 31574 60.2
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 2.023 2.195 12.65 0.888 0.96 0.359 0.941 2.106 6.77
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 2.02 42.31 1.34 31562 2022 54.3 0.207 0.2038 0.2028 0.2541 0.2518 63.72
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 19.9059 f_angle_d 0.6484 f_chiral_restr 0.0372 f_plane_restr 0.0057 f_bond_d 0.0052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3712 Nucleic Acid Atoms 1362 Solvent Atoms 100 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHASER phasing