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Human dead-box RNA helicase DDX19, in complex with an ATP-analogue and RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EWS PDB ENTRY 3EWS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 277 14% PEGMME 2000, 0.25M trimethylamine n-oxide, 0.1 M Tris, pH 8, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.1 41.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.57 α = 90 b = 81.08 β = 90 c = 124.74 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM Q315r monochromator crystals, Si(311) cut and Si(111) 2008-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97931 ESRF ID29
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 2.7 30 99.3 0.145 0.189 9.1 3.3 12073 12073
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 2.7 2.77 99.7 0.55 0.65 2.5 3.2 880
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 3EWS 2.7 29.62 11474 11474 600 99.39 0.22014 0.22014 0.21722 0.222 0.2752 0.2817 RANDOM 12.175
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 0.02 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.56 r_dihedral_angle_3_deg 17.833 r_dihedral_angle_4_deg 15.903 r_dihedral_angle_1_deg 6.018 r_scangle_it 1.41 r_angle_refined_deg 1.129 r_angle_other_deg 0.811 r_scbond_it 0.776 r_mcangle_it 0.456 r_mcbond_it 0.238
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.56 r_dihedral_angle_3_deg 17.833 r_dihedral_angle_4_deg 15.903 r_dihedral_angle_1_deg 6.018 r_scangle_it 1.41 r_angle_refined_deg 1.129 r_angle_other_deg 0.811 r_scbond_it 0.776 r_mcangle_it 0.456 r_mcbond_it 0.238 r_chiral_restr 0.06 r_mcbond_other 0.036 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3225 Nucleic Acid Atoms 125 Solvent Atoms Heterogen Atoms 38
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling