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Crystal structure of the DDX41 DEAD domain in an apo closed form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FE2 PDB ENTRY 3FE2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 DL-malic acid
Crystal Properties Matthews coefficient Solvent content 2.57 52.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.83 α = 90 b = 81.83 β = 90 c = 69.57 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 100 PIXEL DECTRIS PILATUS 6M 2014-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.987 SLS X10SA
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 1.5 50.01 99.9 0.065 18.4 10.34 41380
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 1.5 1.51
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 FREE R-VALUE PDB ENTRY 3FE2 1.5 50.01 41380 2173 99.94 0.18205 0.18069 0.1834 0.20806 0.21 RANDOM 30.416
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] -0.8 -0.4 -0.8 2.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.306 r_dihedral_angle_4_deg 15.737 r_dihedral_angle_3_deg 13.629 r_long_range_B_other 8.399 r_long_range_B_refined 8.359 r_scangle_other 6.626 r_dihedral_angle_1_deg 5.78 r_scbond_it 4.469 r_scbond_other 4.459 r_mcangle_it 4.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.306 r_dihedral_angle_4_deg 15.737 r_dihedral_angle_3_deg 13.629 r_long_range_B_other 8.399 r_long_range_B_refined 8.359 r_scangle_other 6.626 r_dihedral_angle_1_deg 5.78 r_scbond_it 4.469 r_scbond_other 4.459 r_mcangle_it 4.34 r_mcangle_other 4.339 r_mcbond_it 2.969 r_mcbond_other 2.962 r_angle_refined_deg 2.182 r_angle_other_deg 1.089 r_chiral_restr 0.128 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1826 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement PHASER phasing REFMAC model building XDS data scaling XDS data reduction XDS data processing XDS data extraction XDS data collection