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Human DEAD-box RNA helicase DDX10, DEAD domain in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GXS PDB entry 2GXS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 20% Ethanol, 50mM Sodium chloride, 100mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.33 63.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.5 α = 90 b = 63.5 β = 90 c = 304.01 γ = 120
Symmetry Space Group P 61 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 MARRESEARCH Multilayer mirror 2007-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.04123 MAX II I911-2
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 2.15 30 99.7 0.048 0.017 54.1 25.4 20889 20889
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 2.15 2.3 100 0.16 0.047 24.5 26.5 3719
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2GXS 2.15 29.3 19842 19842 1045 100 0.21156 0.20973 0.24757 0.2953 RANDOM 38.392
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.855 r_dihedral_angle_3_deg 15.813 r_dihedral_angle_4_deg 15.476 r_dihedral_angle_1_deg 6.684 r_scangle_it 3.49 r_scbond_it 2.248 r_angle_refined_deg 1.695 r_mcangle_it 1.564 r_angle_other_deg 1.034 r_mcbond_it 0.949
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.855 r_dihedral_angle_3_deg 15.813 r_dihedral_angle_4_deg 15.476 r_dihedral_angle_1_deg 6.684 r_scangle_it 3.49 r_scbond_it 2.248 r_angle_refined_deg 1.695 r_mcangle_it 1.564 r_angle_other_deg 1.034 r_mcbond_it 0.949 r_symmetry_hbond_refined 0.356 r_symmetry_vdw_other 0.284 r_nbd_refined 0.212 r_mcbond_other 0.202 r_nbd_other 0.196 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.171 r_symmetry_vdw_refined 0.104 r_chiral_restr 0.099 r_nbtor_other 0.096 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 1814 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XSCALE data scaling MOLREP phasing