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Insights into RNA/DNA hybrid recognition and processing by RNase H from the crystal structure of a non-specific enzyme-dsDNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZBI PDB ENTRY 1ZBI, using one protein molecule.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 0.1 M sodium acetate, 8 % (w/v) PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.79 55.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.397 α = 90 b = 66.66 β = 122.31 c = 76.926 γ = 90
Symmetry Space Group C 1 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 MARMOSAIC 225 mm CCD 2007-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97850 APS 21-ID-F
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 1.8 50 97.3 0.061 12.4 7.7 38816 37768
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) 1.8 1.86 94.7 0.248 12.4 7.3 3643
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1ZBI, using one protein molecule. 1.8 41.59 35877 1886 99.99 0.21539 0.21396 0.2147 0.24108 0.241 RANDOM 31.474
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] -1.44 -1.42 -1.4 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.558 r_dihedral_angle_4_deg 17.274 r_dihedral_angle_3_deg 16.627 r_dihedral_angle_1_deg 5.925 r_scangle_it 3.633 r_scbond_it 2.448 r_mcangle_it 1.862 r_angle_refined_deg 1.672 r_mcbond_it 1.042 r_chiral_restr 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.558 r_dihedral_angle_4_deg 17.274 r_dihedral_angle_3_deg 16.627 r_dihedral_angle_1_deg 5.925 r_scangle_it 3.633 r_scbond_it 2.448 r_mcangle_it 1.862 r_angle_refined_deg 1.672 r_mcbond_it 1.042 r_chiral_restr 0.12 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2169 Nucleic Acid Atoms 486 Solvent Atoms 166 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing CNS refinement