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TetR(D) in complex with anhydrotetracycline and magnesium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TRT PDB ENTRY 2TRT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 50 MM TRIS-HCL PH 9.0, 1 M (NH4)2SO4, 70 MM NACL, 10 MM MGCL2
Crystal Properties Matthews coefficient Solvent content 2.07 40.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.628 α = 90 b = 65.628 β = 90 c = 178.598 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 RAYONIX SX-165mm MIRRORS 2004-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 1.55 28.9 99.2 0.06 26.5 10.8 28546 -3 28.7
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 1.55 1.65 99.4 1.08 2.94 10.4
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 2TRT 1.55 61.6 27199 1347 99.24 0.17816 0.17627 0.1886 0.21669 0.2184 RANDOM 29.096
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] 0.47 0.47 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.589 r_dihedral_angle_4_deg 16.638 r_dihedral_angle_3_deg 13.342 r_dihedral_angle_1_deg 5.39 r_mcangle_it 2.864 r_scbond_it 2.765 r_angle_refined_deg 2.051 r_mcbond_it 1.955 r_mcbond_other 1.954 r_angle_other_deg 0.907
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.589 r_dihedral_angle_4_deg 16.638 r_dihedral_angle_3_deg 13.342 r_dihedral_angle_1_deg 5.39 r_mcangle_it 2.864 r_scbond_it 2.765 r_angle_refined_deg 2.051 r_mcbond_it 1.955 r_mcbond_other 1.954 r_angle_other_deg 0.907 r_chiral_restr 0.258 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1641 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling AMoRE phasing