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DDX3X bound to ATP analog and remodeled RNA:DNA hybrid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PXA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.1 M HEPEs pH 7.5, 16% PEG 3350, 0.1 M Li3Citrate, 0.1 M Na3Citrate, 2% benzamidine-HCl, 5 mM ADP-BeF3
Crystal Properties Matthews coefficient Solvent content 4.91 74.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.476 α = 90 b = 114.476 β = 90 c = 281.793 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 CCD RAYONIX MX300-HS 2016-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 50 99.7 0.113 0.121 0.044 20.7 7 43593 85.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 99.7 0.882 0.964 0.379 0.641 1.6 6.2
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 THROUGHOUT 4PXA 3.001 40.54 1.34 43572 2197 99.72 0.2112 0.2096 0.2117 0.2412 0.2399 89.6588
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 5.983 f_angle_d 1.083 f_chiral_restr 0.054 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7006 Nucleic Acid Atoms 582 Solvent Atoms 8 Heterogen Atoms 64
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing Coot model building PDB_EXTRACT data extraction