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Structure of Gh-TDH with Additional N-Terminus in Complex with Double-Stranded DNA Containing a 2-Nucleotide 5' Overhang
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WX3 Thermostable direct hemolysin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 25% v/v PEG3350, 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.66 53.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.706 α = 90 b = 79.706 β = 90 c = 74.849 γ = 90
Symmetry Space Group P 4 21 2
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 RAYONIX MX300HE 2021-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
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 1.37 25.22 100 0.045 47.84 8.9 51031
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 1.37 1.42 0.487
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.37 25.22 47798 2617 98.75 0.18667 0.18601 0.1861 0.1991 0.1992 RANDOM 16.085
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_3_deg 11.114 r_dihedral_angle_2_deg 7.353 r_dihedral_angle_1_deg 6.956 r_long_range_B_refined 4.723 r_long_range_B_other 4.458 r_scangle_other 2.486 r_mcangle_it 1.631 r_mcangle_other 1.63 r_scbond_it 1.48 r_scbond_other 1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.114 r_dihedral_angle_2_deg 7.353 r_dihedral_angle_1_deg 6.956 r_long_range_B_refined 4.723 r_long_range_B_other 4.458 r_scangle_other 2.486 r_mcangle_it 1.631 r_mcangle_other 1.63 r_scbond_it 1.48 r_scbond_other 1.48 r_angle_refined_deg 1.175 r_mcbond_it 0.941 r_mcbond_other 0.939 r_angle_other_deg 0.476 r_chiral_restr 0.052 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.004 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 1258 Nucleic Acid Atoms 243 Solvent Atoms 212 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling MOLREP phasing HKL-2000 data reduction