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TetR(D) T103A mutant in complex with minocycline and magnesium
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 6.5 295 Precipitant: 0.1 M MES pH 6.5, 24% PEG 400, 70 mM MgCl2. Protein: 14.55 mg/mL protein in 100mM NaCl, 50 mM Tris buffer, pH 8.0, with 2mM MinoTc, 0.38 uL 3M MgCl2. Precipitant/protein 1/4.
Crystal Properties Matthews coefficient Solvent content 2.23 44.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.81 α = 90 b = 67.81 β = 90 c = 180.16 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 MX-225 NULL 2011-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.950000 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 2.1 57 93.9 0.049 20.15 6.85 11944 50
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 2.1 2.23 95.9 0.54 6.7
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 2TCT 2.1 42.36 10762 1148 93.65 0.23274 0.22775 0.2325 0.28008 0.2847 RANDOM 53.701
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] 3.27 3.27 -6.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.857 r_dihedral_angle_4_deg 18.894 r_dihedral_angle_3_deg 18.283 r_dihedral_angle_1_deg 7.169 r_long_range_B_refined 7.094 r_long_range_B_other 7.091 r_mcangle_it 4.503 r_mcangle_other 4.501 r_scangle_other 4.332 r_mcbond_it 2.965
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.857 r_dihedral_angle_4_deg 18.894 r_dihedral_angle_3_deg 18.283 r_dihedral_angle_1_deg 7.169 r_long_range_B_refined 7.094 r_long_range_B_other 7.091 r_mcangle_it 4.503 r_mcangle_other 4.501 r_scangle_other 4.332 r_mcbond_it 2.965 r_mcbond_other 2.957 r_scbond_it 2.737 r_scbond_other 2.735 r_angle_refined_deg 1.921 r_angle_other_deg 1.411 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1555 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing