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Crystal structure of DEAD-box protein Dbp2 in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8ARK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 2.02 M (NH4)2SO4
100 mM Tris pH 7.0
150 mM Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.82 56.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.939 α = 90 b = 168.843 β = 90 c = 168.87 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 100 PIXEL DECTRIS PILATUS 6M 2019-12-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17B1 0.979300 SSRF BL17B1
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 3.046 119.4 96.2 0.153 0.159 0.044 0.998 11.2 13.2 1019758
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 3.046 3.099 100 1.284 1.355 0.362 0.688 2.1 13.4
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 8ARK 3.05 119.4 4.92 77290 3782 96.2 0.6542 0.2226 0.2272 0.2704 0.2728 110.1
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 10.7136 f_angle_d 0.9978 f_chiral_restr 0.0538 f_plane_restr 0.0093 f_bond_d 0.0046
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21089 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 205
Software Software Software Name Purpose PHENIX refinement PHENIX refinement autoPROC data reduction Aimless data scaling PHASER phasing