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Structure of the human DDX6 C-terminal domain in complex with an EDC3- FDF peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S2M PDB ENTRY 1S2M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M CAPS PH 10.5, 1.2 M NAH2PO4, 0.8 M K2HPO4, 0.2 M LI2SO4
Crystal Properties Matthews coefficient Solvent content 2.74 55.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.63 α = 90 b = 47.85 β = 96.35 c = 65.78 γ = 90
Symmetry Space Group C 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 90 CCD MARRESEARCH MIRRORS 2008-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 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 2.3 46.1 98.4 0.1 10.8 2.9 22482 29.9
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 2.3 2.36 99.7 0.56 2.6 2.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1S2M 2.3 46.08 22482 1201 98.37 0.19319 0.18965 0.2596 0.2436 RANDOM 27.239
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 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.259 r_dihedral_angle_3_deg 16.92 r_dihedral_angle_4_deg 16.354 r_dihedral_angle_1_deg 7.121 r_scangle_it 4.811 r_scbond_it 2.956 r_mcangle_it 2.019 r_angle_refined_deg 1.728 r_mcbond_it 1.043 r_chiral_restr 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.259 r_dihedral_angle_3_deg 16.92 r_dihedral_angle_4_deg 16.354 r_dihedral_angle_1_deg 7.121 r_scangle_it 4.811 r_scbond_it 2.956 r_mcangle_it 2.019 r_angle_refined_deg 1.728 r_mcbond_it 1.043 r_chiral_restr 0.111 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3144 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing