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Crystal Structure of human DEAD-box RNA helicase DDX3X
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WRB PDB ENTRY 1WRB for the DEAD domain and 2DB3 for the helicase domain experimental model PDB 2DB3 PDB ENTRY 1WRB for the DEAD domain and 2DB3 for the helicase domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 277 1.75M Na formate, 0.1M Tris pH 7.5, 20mM ATPgS and MgCl2, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.51 64.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.288 α = 90 b = 67.288 β = 90 c = 253.47 γ = 120
Symmetry Space Group P 31 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 100 CCD ADSC QUANTUM 315 2006-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.072 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 14.91 99.2 10.6 32841 32841
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 98.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 THROUGHOUT PDB ENTRY 1WRB for the DEAD domain and 2DB3 for the helicase domain 2.2 14.91 33112 32841 1751 99.18 0.18719 0.18873 0.18719 0.1806 0.21822 0.2111 RANDOM 52.846
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] 1.91 0.96 1.91 -2.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.451 r_dihedral_angle_4_deg 18.485 r_dihedral_angle_3_deg 15.979 r_dihedral_angle_1_deg 6.456 r_scangle_it 4.166 r_scbond_it 2.656 r_mcangle_it 1.65 r_angle_refined_deg 1.584 r_mcbond_it 1.027 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.451 r_dihedral_angle_4_deg 18.485 r_dihedral_angle_3_deg 15.979 r_dihedral_angle_1_deg 6.456 r_scangle_it 4.166 r_scbond_it 2.656 r_mcangle_it 1.65 r_angle_refined_deg 1.584 r_mcbond_it 1.027 r_nbtor_refined 0.306 r_nbd_refined 0.214 r_symmetry_hbond_refined 0.202 r_xyhbond_nbd_refined 0.183 r_symmetry_vdw_refined 0.154 r_chiral_restr 0.113 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3243 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement DNA data collection XDS data reduction XSCALE data scaling MOLREP phasing