6RXB

Crystal structure of TetR-Q116A from Acinetobacter baumannii AYE in complex with minocycline


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6RX9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION5.52910.1M Sodium cacodylate, pH5.5, 11% PEG Smear Broad, 3% Tacsimate, pH7.0, and 10% Ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.2946.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.543α = 90
b = 64.227β = 90
c = 220.954γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2018-04-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.979SOLEILPROXIMA 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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.2548.411000.2560.2670.0720.991613.743315
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.321000.5480.65214

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6RX92.2548.4141073215199.950.242150.240390.27596RANDOM52.613
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.984
r_dihedral_angle_4_deg13.603
r_dihedral_angle_3_deg13.327
r_dihedral_angle_1_deg12.531
r_long_range_B_refined2.69
r_long_range_B_other2.69
r_angle_refined_deg1.148
r_angle_other_deg1.032
r_mcangle_it0.374
r_mcangle_other0.374
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.984
r_dihedral_angle_4_deg13.603
r_dihedral_angle_3_deg13.327
r_dihedral_angle_1_deg12.531
r_long_range_B_refined2.69
r_long_range_B_other2.69
r_angle_refined_deg1.148
r_angle_other_deg1.032
r_mcangle_it0.374
r_mcangle_other0.374
r_mcbond_it0.197
r_mcbond_other0.197
r_scangle_other0.179
r_scbond_it0.083
r_scbond_other0.083
r_chiral_restr0.031
r_gen_planes_refined0.002
r_bond_refined_d0.001
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms5911
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms150

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing