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Crystal structure of TetR-Q116A from Acinetobacter baumannii AYE in complex with minocycline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RX9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 5.5 291 0.1M Sodium cacodylate, pH5.5, 11% PEG Smear Broad, 3% Tacsimate, pH7.0, and 10% Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.29 46.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.543 α = 90 b = 64.227 β = 90 c = 220.954 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 9M 2018-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.979 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.25 48.41 100 0.256 0.267 0.072 0.991 6 13.7 43315
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.32 100 0.548 0.652 14
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 6RX9 2.25 48.41 41073 2151 99.95 0.24215 0.24039 0.2429 0.27596 0.2798 RANDOM 52.613
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] 2.88 -2.09 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.984 r_dihedral_angle_4_deg 13.603 r_dihedral_angle_3_deg 13.327 r_dihedral_angle_1_deg 12.531 r_long_range_B_refined 2.69 r_long_range_B_other 2.69 r_angle_refined_deg 1.148 r_angle_other_deg 1.032 r_mcangle_it 0.374 r_mcangle_other 0.374
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.984 r_dihedral_angle_4_deg 13.603 r_dihedral_angle_3_deg 13.327 r_dihedral_angle_1_deg 12.531 r_long_range_B_refined 2.69 r_long_range_B_other 2.69 r_angle_refined_deg 1.148 r_angle_other_deg 1.032 r_mcangle_it 0.374 r_mcangle_other 0.374 r_mcbond_it 0.197 r_mcbond_other 0.197 r_scangle_other 0.179 r_scbond_it 0.083 r_scbond_other 0.083 r_chiral_restr 0.031 r_gen_planes_refined 0.002 r_bond_refined_d 0.001 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 5911 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing