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DEAD-box helicase DbpA bound to single stranded RNA and ADP/BeF3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DB3 2db3, 3moj experimental model PDB 3MOJ 2db3, 3moj
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 20 % (v/v) PEG 3350, 400 mM KSCN, 100 mM Tris, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.46 50.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.643 α = 97.157 b = 121.599 β = 92.426 c = 122.417 γ = 103.438
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 2021-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.9766 EMBL/DESY, HAMBURG X13
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 2.5 56.88 96.62 0.99 7.25 3.6 108844 51.89
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.589 96.52 0.75 1.75 3.6
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 2db3, 3moj 2.5 56.88 1.98 108814 5440 96.62 0.2149 0.2133 0.217 0.2469 0.2486 69.07
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 18.88 f_angle_d 0.834 f_chiral_restr 0.0483 f_plane_restr 0.0045 f_bond_d 0.0035
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20580 Nucleic Acid Atoms 2753 Solvent Atoms 24 Heterogen Atoms 192
Software Software Software Name Purpose PHENIX refinement PHENIX phasing XDS data reduction XDS data scaling Coot model building