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S. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 Mixed 100 nL of the complex at a protein concentration of 16 mg/ml with 100 nL of reservoir solution containing 200 mM Mg(NO3)2 and 18 percent PEG 3350 and incubating 4 days over 100 uL of reservoir solution in a sealed chamber.
Crystal Properties Matthews coefficient Solvent content 2.31 46.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.082 α = 90 b = 91.751 β = 90 c = 104.521 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 315 2014-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.81 104.52 99.6 0.166 10.1 4.8 37530 13.53
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.81 1.91 100 0.886 1.9 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION FREE R-VALUE 1.81 52.26 1.34 37472 1846 99.3 0.177 0.175 0.1755 0.208 0.2073
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 f_dihedral_angle_d 16.459 f_angle_d 1.056 f_chiral_restr 0.067 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3072 Nucleic Acid Atoms 105 Solvent Atoms 325 Heterogen Atoms 51
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction HKL-2000 data reduction