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Human DEAD-box RNA helicase DDX20, DEAD domain in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QVA PDB ENTRY 1QVA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.2 277 12% PEG3350, 200 mM Sodium chloride, 100 mM Bis-Tris, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.5 50.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.8 α = 90 b = 63.8 β = 90 c = 214.3 γ = 120
Symmetry Space Group P 31 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 ADSC QUANTUM 4 Toroidal mirror 2006-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.93300 ESRF ID14-2
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 1.3 40 99.8 0.057 0.057 23.5 10 125192 125192
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) 1.3 1.5 99.9 0.458 0.233 5.2 9.6 43117
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 1QVA 1.3 38.46 119028 119028 6264 100 0.15378 0.15378 0.15268 0.1642 0.17485 0.1858 RANDOM 9.989
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] 0.1 0.05 0.1 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.689 r_dihedral_angle_4_deg 15.543 r_dihedral_angle_3_deg 11.201 r_sphericity_free 5.597 r_dihedral_angle_1_deg 5.11 r_scangle_it 3.206 r_scbond_it 2.471 r_sphericity_bonded 2.469 r_mcangle_it 1.537 r_angle_refined_deg 1.443
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.689 r_dihedral_angle_4_deg 15.543 r_dihedral_angle_3_deg 11.201 r_sphericity_free 5.597 r_dihedral_angle_1_deg 5.11 r_scangle_it 3.206 r_scbond_it 2.471 r_sphericity_bonded 2.469 r_mcangle_it 1.537 r_angle_refined_deg 1.443 r_mcbond_it 1.314 r_rigid_bond_restr 1.114 r_angle_other_deg 0.926 r_mcbond_other 0.414 r_symmetry_vdw_other 0.309 r_nbd_refined 0.209 r_nbd_other 0.186 r_symmetry_hbond_refined 0.186 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.143 r_symmetry_vdw_refined 0.092 r_nbtor_other 0.084 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3227 Nucleic Acid Atoms Solvent Atoms 668 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XDS data scaling MOLREP phasing