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5-Se-T2/4-DNA and native 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 2G8U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1M MES pH 6.5, 12%(w/v) PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.36 47.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.952 α = 90 b = 37.827 β = 96.2 c = 62.07 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 315r 2016-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 50 100 0.023 31.5 7.3 20662
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 2g8u 1.7 35.506 19632 1030 99.85 0.1805 0.17843 0.1892 0.22128 0.2244 RANDOM 22.106
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 r_dihedral_angle_2_deg 34.82 r_dihedral_angle_3_deg 13.986 r_dihedral_angle_4_deg 13.811 r_long_range_B_refined 7.629 r_long_range_B_other 7.054 r_dihedral_angle_1_deg 6.703 r_scangle_other 4.671 r_scbond_it 3.169 r_scbond_other 3.168 r_mcangle_other 3.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.82 r_dihedral_angle_3_deg 13.986 r_dihedral_angle_4_deg 13.811 r_long_range_B_refined 7.629 r_long_range_B_other 7.054 r_dihedral_angle_1_deg 6.703 r_scangle_other 4.671 r_scbond_it 3.169 r_scbond_other 3.168 r_mcangle_other 3.017 r_mcangle_it 3.015 r_angle_refined_deg 2.128 r_mcbond_it 2.087 r_mcbond_other 2.073 r_angle_other_deg 1.395 r_chiral_restr 0.138 r_bond_other_d 0.024 r_bond_refined_d 0.021 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1076 Nucleic Acid Atoms 247 Solvent Atoms 76 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing