5ENQ

MBX3132 bound structure of bacterial efflux pump.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.1 MES pH6.5, 0.21 M NaCl, 11.5% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.8356.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.726α = 90
b = 145.517β = 90
c = 173.452γ = 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 10.97857SOLEILPROXIMA 1

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
11.85099.80.1060.99912.969251472
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)
11.81.91991.9490.4848.7

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 REPLACEMENTTHROUGHOUT5EN51.8502388591240899.960.183870.181860.22291RANDOM36.829
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]
1.25-0.69-0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.353
r_dihedral_angle_4_deg19.158
r_dihedral_angle_3_deg13.497
r_long_range_B_refined8.529
r_long_range_B_other8.476
r_scangle_other6.81
r_dihedral_angle_1_deg6.166
r_mcangle_it4.502
r_mcangle_other4.502
r_scbond_it4.481
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.353
r_dihedral_angle_4_deg19.158
r_dihedral_angle_3_deg13.497
r_long_range_B_refined8.529
r_long_range_B_other8.476
r_scangle_other6.81
r_dihedral_angle_1_deg6.166
r_mcangle_it4.502
r_mcangle_other4.502
r_scbond_it4.481
r_scbond_other4.481
r_mcbond_it3.27
r_mcbond_other3.27
r_angle_refined_deg1.808
r_angle_other_deg1.022
r_chiral_restr0.114
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms16867
Nucleic Acid Atoms
Solvent Atoms1355
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing