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Human DEAD-BOX RNA helicase DDX5 (P68), conserved domain I in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I4I PDB ENTRY 2I4I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 277 17.5% PEG3350, 0.25M Lithium Sulfate, 0.1M Bis-Tris, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.43 49.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.57 α = 90 b = 106.87 β = 90 c = 117.32 γ = 90
Symmetry Space Group C 2 2 21
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 MX-225 mirrors 2008-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 2.6 35 99.4 0.142 0.188 11 4 16601 16601
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) 2.6 2.67 99.8 0.742 0.728 2.44 4 1211
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 (All) 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 PDB ENTRY 2I4I 2.6 31.91 15770 15770 831 100 0.2084 0.2084 0.20494 0.2077 0.27283 0.2724 RANDOM 22.991
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] 1.08 -1.22 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.689 r_dihedral_angle_3_deg 18.504 r_dihedral_angle_4_deg 15.821 r_dihedral_angle_1_deg 5.863 r_scangle_it 2.369 r_scbond_it 1.376 r_angle_refined_deg 1.354 r_mcangle_it 0.979 r_angle_other_deg 0.877 r_mcbond_it 0.501
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.689 r_dihedral_angle_3_deg 18.504 r_dihedral_angle_4_deg 15.821 r_dihedral_angle_1_deg 5.863 r_scangle_it 2.369 r_scbond_it 1.376 r_angle_refined_deg 1.354 r_mcangle_it 0.979 r_angle_other_deg 0.877 r_mcbond_it 0.501 r_mcbond_other 0.088 r_chiral_restr 0.074 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3696 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 70
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling