6ZO6

Minocycline binding to the deep binding pocket of AcrB-G619P


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, 0.0012M MINOCYCLINE
Crystal Properties
Matthews coefficientSolvent content
3.6666.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.281α = 90
b = 161.008β = 90
c = 245.457γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2014-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.979SOLEILPROXIMA 1

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
12.3549.361000.1630.1810.0770.9948.65.4240294
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)
12.352.3999.91.9682.1770.9230.40815.5

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 REPLACEMENTTHROUGHOUT5JMN2.3549.362281041207899.970.23240.23110.2572RANDOM44.408
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]
-2.352.74-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.878
r_dihedral_angle_4_deg15.719
r_dihedral_angle_3_deg13.923
r_dihedral_angle_1_deg5.101
r_angle_refined_deg1.17
r_angle_other_deg1.018
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_deg29.878
r_dihedral_angle_4_deg15.719
r_dihedral_angle_3_deg13.923
r_dihedral_angle_1_deg5.101
r_angle_refined_deg1.17
r_angle_other_deg1.018
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 Atoms25984
Nucleic Acid Atoms
Solvent Atoms1188
Heterogen Atoms882

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction