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Structure of Gh-TDH in Complex with 10-nt match Double-Stranded DNA
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 PEG 3350, 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.76 55.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.728 α = 90 b = 79.728 β = 90 c = 75.428 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 Sym 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 1.42 25.07 99.7 0.058 31.73 7.9 46138
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.42 1.47 0.588
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 1.42 25.07 43011 2292 98.14 0.18541 0.18458 0.1925 0.20124 0.204 RANDOM 17.177
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.945 r_dihedral_angle_1_deg 7.086 r_long_range_B_refined 5.481 r_long_range_B_other 5.314 r_dihedral_angle_2_deg 4.555 r_scangle_other 3.526 r_scbond_it 2.133 r_scbond_other 2.132 r_mcangle_it 2.049 r_mcangle_other 2.048
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.945 r_dihedral_angle_1_deg 7.086 r_long_range_B_refined 5.481 r_long_range_B_other 5.314 r_dihedral_angle_2_deg 4.555 r_scangle_other 3.526 r_scbond_it 2.133 r_scbond_other 2.132 r_mcangle_it 2.049 r_mcangle_other 2.048 r_angle_refined_deg 1.236 r_mcbond_it 1.234 r_mcbond_other 1.229 r_angle_other_deg 0.414 r_chiral_restr 0.054 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001 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 1262 Nucleic Acid Atoms 202 Solvent Atoms 174 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling MOLREP phasing HKL-2000 data reduction