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Human DEAD-box RNA helicase DDX41, helicase domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I4I PDB ENTRY 2I4I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 293 25% PEG 3350, 200mM Lithium sulfate, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 5.50
Crystal Properties Matthews coefficient Solvent content 2.41 48.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.013 α = 90 b = 68.013 β = 90 c = 305.604 γ = 120
Symmetry Space Group P 65 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 ADSC QUANTUM 315 DOUBLE CRYSTAL, SI(111) OR SI(311), TOROIDAL MIRROR 2006-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.6 30 99.9 0.103 0.029 35.9 40 13827
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.8 100 0.45 0.084 12.6 41.8
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2I4I 2.6 29.72 13220 696 100 0.24594 0.24345 0.2472 0.29431 0.2934 RANDOM 47.341
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.956 r_dihedral_angle_4_deg 24.418 r_dihedral_angle_3_deg 18.747 r_dihedral_angle_1_deg 6.343 r_scangle_it 2.548 r_scbond_it 1.612 r_angle_refined_deg 1.602 r_mcangle_it 0.942 r_angle_other_deg 0.909 r_mcbond_it 0.635
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.956 r_dihedral_angle_4_deg 24.418 r_dihedral_angle_3_deg 18.747 r_dihedral_angle_1_deg 6.343 r_scangle_it 2.548 r_scbond_it 1.612 r_angle_refined_deg 1.602 r_mcangle_it 0.942 r_angle_other_deg 0.909 r_mcbond_it 0.635 r_nbd_refined 0.25 r_symmetry_vdw_other 0.246 r_symmetry_hbond_refined 0.218 r_symmetry_vdw_refined 0.216 r_nbd_other 0.196 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.15 r_mcbond_other 0.123 r_nbtor_other 0.093 r_chiral_restr 0.084 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2481 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing