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Structure of A. thaliana TBP bound to TBP-TG_P nicked DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9OW7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% (w/v) PEG 3350, 0.1 M Citric acid pH 5.0 and 0.2 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.67 54.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.117 α = 90 b = 117.524 β = 106.94 c = 102.066 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M 2024-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.6 48.6 97.7 0.083 0.055 0.994 9.6 3.3 46965
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 0.508 0.321 0.794 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.6 48.57 1.34 46919 2344 97.65 0.2049 0.2024 0.2048 0.2533 0.2532
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 f_dihedral_angle_d 14.745 f_angle_d 1.057 f_chiral_restr 0.062 f_plane_restr 0.011 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8733 Nucleic Acid Atoms 816 Solvent Atoms 278 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction MOLREP phasing PDB_EXTRACT data extraction