5ENS

Rhodamine bound structure of bacterial efflux pump.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.1 MES pH6.5, 0.21M NaCl, 11.5% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.8556.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.652α = 90
b = 145.245β = 90
c = 174.148γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.85099.70.2850.9585.166.768419
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.9798.91.2730.4196.6

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 REPLACEMENTTHROUGHOUT5en52.85065042337599.840.197230.194110.25803RANDOM42.889
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]
1.94-1.51-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.282
r_dihedral_angle_4_deg16.556
r_dihedral_angle_3_deg15.127
r_long_range_B_refined6.781
r_long_range_B_other6.775
r_dihedral_angle_1_deg6.335
r_scangle_other4.433
r_mcangle_other4.228
r_mcangle_it4.227
r_scbond_it2.618
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.282
r_dihedral_angle_4_deg16.556
r_dihedral_angle_3_deg15.127
r_long_range_B_refined6.781
r_long_range_B_other6.775
r_dihedral_angle_1_deg6.335
r_scangle_other4.433
r_mcangle_other4.228
r_mcangle_it4.227
r_scbond_it2.618
r_scbond_other2.618
r_mcbond_it2.545
r_mcbond_other2.54
r_angle_refined_deg1.493
r_angle_other_deg0.943
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.002
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 Atoms16724
Nucleic Acid Atoms
Solvent Atoms253
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing