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DEAD-box helicase DbpA in the active conformation bound to a ss/dsRNA junction and ADP/BeF3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PMQ PDB Deposition D_1292103740
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 293 0.2 M di-Sodium tartate, 20 %(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.24 61.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.69 α = 90 b = 169.69 β = 90 c = 111.99 γ = 90
Symmetry Space Group P 42 21 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 2019-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 48.39 99.92 0.1208 0.1225 0.02 0.998 24.34 36.15 33298 95.07
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 3 3.107 99.79 1.043 0.27 0.913 3.11
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 PDB Deposition D_1292103740 3 48.39 1.38 33285 1664 99.97 0.1985 0.1971 0.2021 0.2246 0.2309 116.82
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 17.0975 f_angle_d 0.7665 f_chiral_restr 0.053 f_plane_restr 0.0044 f_bond_d 0.0035
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6779 Nucleic Acid Atoms 1836 Solvent Atoms 8 Heterogen Atoms 64
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction XDS data scaling PHENIX phasing