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DEAD-box helicase DbpA in the active conformation bound to a hairpin loop RNA and ADP/BeF3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DB3 2DB3 and 3MOJ experimental model PDB 3MOJ 2DB3 and 3MOJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 200 mM NH4/tartrate
100 mM Tris, pH 8.0
20% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.58 52.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.644 α = 90 b = 159.644 β = 90 c = 204.682 γ = 90
Symmetry Space Group P 43 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 2019-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00 SLS X06SA
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 3.22 49.42 99.7 0.245 0.255 0.999 10.7 13.6 43424 88.86
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 3.22 3.33 99.65 1.79 1.86 0.553 1.42
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2DB3 and 3MOJ 3.22 49.42 1.34 43395 2172 99.76 0.2294 0.2276 0.2301 0.2636 0.2619 Random 86.14
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 15.538 f_angle_d 0.587 f_chiral_restr 0.0399 f_plane_restr 0.0038 f_bond_d 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13797 Nucleic Acid Atoms 3568 Solvent Atoms Heterogen Atoms 128
Software Software Software Name Purpose PHENIX refinement PHENIX phasing Coot model building XDS data reduction XSCALE data scaling