6ZOC

Erythromycin binding to the access pocket of AcrB-G616P L protomer and 3-formylrifamycin SV binding to the access pocket of AcrB-G616P T protomer


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, 0.003M RIFAMPICIN, 0.001M ERYTHROMYCIN, 0.001M FUSIDIC ACID, 0.001M LINEZOLID, 0.001M OXACILLIN
Crystal Properties
Matthews coefficientSolvent content
3.5965.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.327α = 90
b = 161.26β = 90
c = 244.023γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-06-06MSINGLE 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
12.8949.431000.6040.640.210.9934.69.112962348.59
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)
12.892.941006.3746.7572.2250.4060.59

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 REPLACEMENTTHROUGHOUT5JMN2.8949.3788443439967.70.21930.21840.2381RANDOM38.13
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]
-4.24344.9007-0.6573
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion16.86
t_omega_torsion1.95
t_angle_deg0.54
t_bond_d0.005
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms25903
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms523

Software

Software
Software NamePurpose
BUSTERrefinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction