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How an in vitro selected peptide mimics the antibiotic tetracycline to induce TET repressor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TCT PDB ENTRY 2TCT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 292 4M sodium formate, 0.1M Tris-HCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.49 50.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.89 α = 90 b = 200.59 β = 90 c = 65.28 γ = 90
Symmetry Space Group P 21 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2004-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.918 BESSY 14.2
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 2.55 40 99.4 0.09 14.93 33932 -3 43.938
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 2.55 2.71 98.2 0.483 3.7 5316
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 PDB ENTRY 2TCT 2.55 30 33914 2713 100 0.211 0.206 0.2145 0.27 0.2738 RANDOM 46.989
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] 1.52 -3.15 1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.724 r_dihedral_angle_3_deg 19.243 r_dihedral_angle_4_deg 16.824 r_dihedral_angle_1_deg 6.2 r_scangle_it 1.91 r_angle_refined_deg 1.38 r_scbond_it 1.252 r_angle_other_deg 0.841 r_mcangle_it 0.824 r_mcbond_it 0.691
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.724 r_dihedral_angle_3_deg 19.243 r_dihedral_angle_4_deg 16.824 r_dihedral_angle_1_deg 6.2 r_scangle_it 1.91 r_angle_refined_deg 1.38 r_scbond_it 1.252 r_angle_other_deg 0.841 r_mcangle_it 0.824 r_mcbond_it 0.691 r_symmetry_vdw_other 0.248 r_nbd_refined 0.234 r_nbtor_refined 0.187 r_nbd_other 0.174 r_symmetry_vdw_refined 0.157 r_xyhbond_nbd_refined 0.138 r_mcbond_other 0.101 r_symmetry_hbond_refined 0.099 r_nbtor_other 0.091 r_chiral_restr 0.074 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6884 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection XDS data reduction AMoRE phasing