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Crystal structure of the DDX41 DEAD domain in an apo open form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GVR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 tri-ammonium citrate,
PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.26 45.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.188 α = 90 b = 50.96 β = 95.51 c = 202.599 γ = 90
Symmetry Space Group I 1 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 RAYONIX MX225HE 2014-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 0.979 SPring-8 BL32XU
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 2.2 49.41 76.5 0.202 9.3 4.4 36258
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 2.27
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 5GVR 2.2 49.41 34370 1824 76.08 0.21071 0.20722 0.214 0.27487 0.2775 RANDOM 24.482
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] 1.7 -0.38 -1.42 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.44 r_dihedral_angle_4_deg 17.157 r_dihedral_angle_3_deg 15.989 r_dihedral_angle_1_deg 6.997 r_long_range_B_refined 6.053 r_long_range_B_other 6.042 r_mcangle_it 3.396 r_mcangle_other 3.396 r_scangle_other 3.375 r_scbond_it 1.991
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.44 r_dihedral_angle_4_deg 17.157 r_dihedral_angle_3_deg 15.989 r_dihedral_angle_1_deg 6.997 r_long_range_B_refined 6.053 r_long_range_B_other 6.042 r_mcangle_it 3.396 r_mcangle_other 3.396 r_scangle_other 3.375 r_scbond_it 1.991 r_scbond_other 1.991 r_mcbond_it 1.944 r_mcbond_other 1.943 r_angle_refined_deg 1.696 r_angle_other_deg 1.02 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 6473 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX model building MOSFLM data collection MOSFLM data extraction MOSFLM data processing MOSFLM data reduction Aimless data scaling PHASER phasing