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Crystal structure analysis of TetR(D) complex with doxycycline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TCT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 1.1M AMMONIUM SULPHATE, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.09 41.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.83 α = 90 b = 65.83 β = 90 c = 179.502 γ = 90
Symmetry Space Group I 41 2 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 MAR CCD 165 mm 2004-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8011 EMBL/DESY, HAMBURG X13
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 1.89 19.34 100 0.071 29.6 15.8 16248 16248 29.9
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 1.89 1.93 100 0.36 7.3 10.3 785
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2TCT 1.89 19.34 16248 15374 817 99.75 0.20419 0.20419 0.2021 0.2056 0.24323 0.246 RANDOM 29.971
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] 1.64 1.64 -3.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.103 r_dihedral_angle_3_deg 18.521 r_dihedral_angle_4_deg 16.106 r_dihedral_angle_1_deg 5.56 r_scangle_it 4.233 r_scbond_it 3.097 r_angle_refined_deg 1.974 r_mcangle_it 1.902 r_mcbond_it 1.615 r_angle_other_deg 1.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.103 r_dihedral_angle_3_deg 18.521 r_dihedral_angle_4_deg 16.106 r_dihedral_angle_1_deg 5.56 r_scangle_it 4.233 r_scbond_it 3.097 r_angle_refined_deg 1.974 r_mcangle_it 1.902 r_mcbond_it 1.615 r_angle_other_deg 1.139 r_mcbond_other 0.343 r_symmetry_vdw_refined 0.271 r_symmetry_vdw_other 0.264 r_nbd_refined 0.244 r_nbd_other 0.207 r_symmetry_hbond_refined 0.2 r_nbtor_refined 0.197 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.17 r_metal_ion_refined 0.122 r_nbtor_other 0.102 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1641 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction SCALEPACK data scaling