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Extended 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 2WAX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 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 2.8 56.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.425 α = 90 b = 47.878 β = 96.34 c = 65.757 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 2008-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.978 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.21 25.31 95.6 0.104 9.6 2.9 25958 30.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 2.25 0.467
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 2WAX 2.21 25.31 25943 1314 95.6 0.181 0.179 0.1871 0.226 0.2312 RANDOM 40.05
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] 6.2111 2.9435 -10.3715 4.1604
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.12 t_omega_torsion 3.38 t_angle_deg 1.06 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.12 t_omega_torsion 3.38 t_angle_deg 1.06 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3402 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 115
Software Software Software Name Purpose BUSTER refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing