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Crystal structure of the N-terminal domain of the Human DEAD-BOX RNA helicase DDX5 (P68)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JGN PDB ENTRY 2JGN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 2% (V/V) TACSIMATE PH 4.0, 0.1 M BIS-TRIS PH 6.5, AND 20% (W/V) POLYETHYLENE GLYCOL 3350
Crystal Properties Matthews coefficient Solvent content 2.33 47.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.18 α = 90 b = 73.801 β = 90 c = 104 γ = 90
Symmetry Space Group I 2 2 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 CCD MIRROR 2009-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.7 25 98.9 0.08 19.6 5.9 7229 2 41
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 99.9 0.48 2.7 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2JGN 2.7 24.64 7229 395 99.5 0.262 0.262 0.2617 0.293 RANDOM 76.9
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] -2.81 -6.37 9.18
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.2 c_angle_deg 1.6 c_improper_angle_d 0.95 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.2 c_angle_deg 1.6 c_improper_angle_d 0.95 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2015 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling MrBUMP phasing