6ZOG

Minocycline binding to the deep binding pocket of AcrB-I38F_I671T


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5JMN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.62910.05M ADA, PH 6.6, 0.15-0.25M AMMONIUM SULFATE, 5% GLYCEROL, 8-9% PEG4000, 0.002M MINOCYCLINE
Crystal Properties
Matthews coefficientSolvent content
3.6766.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.965α = 90
b = 161.954β = 90
c = 245.288γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)1.033PETRA III, EMBL c/o DESYP13 (MX1)

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
12.7549.591000.1910.2050.0740.999.87.6151127
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.752.81002.0682.2190.7970.4961.27.7

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 REPLACEMENTTHROUGHOUT5JMN2.7549.59143539749299.980.23220.23030.2682RANDOM61.673
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]
-4.686.93-2.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.009
r_dihedral_angle_4_deg14.879
r_dihedral_angle_3_deg14.16
r_dihedral_angle_1_deg4.669
r_angle_refined_deg1.171
r_angle_other_deg1.03
r_chiral_restr0.032
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.009
r_dihedral_angle_4_deg14.879
r_dihedral_angle_3_deg14.16
r_dihedral_angle_1_deg4.669
r_angle_refined_deg1.171
r_angle_other_deg1.03
r_chiral_restr0.032
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms25924
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms491

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction