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Structure of the C-terminal domain of the DEAD-box protein Dbp5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 2M Na/K HPO4, 100mM Na cacodylate pH 6.5, 8% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.6 52.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.423 α = 90 b = 82.423 β = 90 c = 56.578 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD ADSC QUANTUM 210 2005-11-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 0.9795,1.0332,1.11588 ALS 8.3.1
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 1.7 56.6 100 0.04 3.7 24212 24212 2 2 25.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.8 30 2 19340 1016 99.85 0.19315 0.1913 0.1958 0.22999 0.2302 RANDOM 29.957
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] -0.82 -0.41 -0.82 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.504 r_dihedral_angle_4_deg 18.491 r_dihedral_angle_3_deg 14.028 r_dihedral_angle_1_deg 5.219 r_scangle_it 2.965 r_scbond_it 2.011 r_mcangle_it 1.251 r_angle_refined_deg 0.956 r_mcbond_it 0.851 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.504 r_dihedral_angle_4_deg 18.491 r_dihedral_angle_3_deg 14.028 r_dihedral_angle_1_deg 5.219 r_scangle_it 2.965 r_scbond_it 2.011 r_mcangle_it 1.251 r_angle_refined_deg 0.956 r_mcbond_it 0.851 r_nbtor_refined 0.305 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.156 r_symmetry_hbond_refined 0.149 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1422 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection SOLVE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling