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Crystal structure of Aquifex aeolicus RNase III (D44N) complexed with product of double-stranded RNA processing
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RC7 pdb entries 1RC7, 1YZ9, 1YYW, 1YYO experimental model PDB 1YZ9 pdb entries 1RC7, 1YZ9, 1YYW, 1YYO experimental model PDB 1YYW pdb entries 1RC7, 1YZ9, 1YYW, 1YYO experimental model PDB 1YYO pdb entries 1RC7, 1YZ9, 1YYW, 1YYO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 M ammonium sulfate, 25% w/v PEG 3350 in 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.55 51.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.839 α = 90 b = 50.976 β = 104.47 c = 113.746 γ = 90
Symmetry Space Group P 1 21 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 BRUKER PROTEUM 300 mirror 2005-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
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 2.05 30 90.6 0.061 13.3 2.5 40208 40208 43
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) 2.05 2.12 55.2 0.411 1.6 1.6 2408
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 entries 1RC7, 1YZ9, 1YYW, 1YYO 2.05 29.84 38707 38707 1932 86.8 0.215 0.205 0.205 0.2068 0.258 0.2572 RANDOM 48.8
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] 0.68 8.27 2.01 -2.7
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 16.8 c_scangle_it 6.61 c_scbond_it 5.13 c_mcangle_it 4.68 c_mcbond_it 3.66 c_angle_deg 1.1 c_improper_angle_d 0.97 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 16.8 c_scangle_it 6.61 c_scbond_it 5.13 c_mcangle_it 4.68 c_mcbond_it 3.66 c_angle_deg 1.1 c_improper_angle_d 0.97 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3640 Nucleic Acid Atoms 1196 Solvent Atoms 298 Heterogen Atoms 2
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling PHASES phasing