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Structure of A. thaliana TBP bound to AG-P nicked DNA site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9OWI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 10% (w/v) PEG 8000, 0.1 CHES pH 9.5
Crystal Properties Matthews coefficient Solvent content 2.94 58.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.73 α = 90 b = 106.21 β = 101.1 c = 161.922 γ = 90
Symmetry Space Group I 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 PIXEL DECTRIS PILATUS 6M 2024-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0 ALS 5.0.1
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 2.91 88.3 97.5 0.076 0.049 0.994 8.3 3.3 43821
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 2.91 3.1 0.595 0.384 0.679 1.9
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 2.91 79.66 1.34 43821 2016 97.03 0.2351 0.2342 0.2432 0.2533 0.2607
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 20.261 f_angle_d 1.284 f_chiral_restr 0.065 f_bond_d 0.012 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8595 Nucleic Acid Atoms 2694 Solvent Atoms Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction MOLREP phasing PDB_EXTRACT data extraction