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High resolution structure of DNA/RNA hybrid in complex with RNase H catalytic domain D132N mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TWH PDB entry 3TWH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 0.04 M Magnesium chloride, 0.05 M Sodium cacodylate, 5% MPD, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.36 47.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.301 α = 90 b = 37.672 β = 96.76 c = 62.378 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 ADSC QUANTUM 315 mirrors 2011-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.9765 ALS 5.0.3
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 1.6 61.94 94.1 0.08 16.9 4.8 25140 23657
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 1.6 1.639 94.1 0.08 16.9 4.8 25140
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 3TWH 1.6 30 25140 22402 1201 93.89 0.19589 0.19366 0.1931 0.23463 0.2341 RANDOM 21.836
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] 0.11 -0.58 1.03 -1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.193 r_dihedral_angle_3_deg 14.499 r_dihedral_angle_4_deg 13.428 r_dihedral_angle_1_deg 5.699 r_scangle_it 3.54 r_scbond_it 2.304 r_mcangle_it 1.639 r_angle_refined_deg 1.56 r_mcbond_it 0.882 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.193 r_dihedral_angle_3_deg 14.499 r_dihedral_angle_4_deg 13.428 r_dihedral_angle_1_deg 5.699 r_scangle_it 3.54 r_scbond_it 2.304 r_mcangle_it 1.639 r_angle_refined_deg 1.56 r_mcbond_it 0.882 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1085 Nucleic Acid Atoms 249 Solvent Atoms 124 Heterogen Atoms 4
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling