5ENO

MBX2319 bound structure of bacterial efflux pump.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.1 M MES pH6.5, 0.21 M NaCl, 11.5% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.856.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.758α = 90
b = 145.147β = 90
c = 174.243γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.97794SLSX06DA

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
12.25099.70.3070.9845.2713.6140556
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)
12.22.3398.51.630.47312.2

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 REPLACEMENTTHROUGHOUT5EN52.250133115685699.910.20160.199280.24706RANDOM32.733
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]
1.29-1.350.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.057
r_dihedral_angle_4_deg19.096
r_dihedral_angle_3_deg14.682
r_long_range_B_other7.453
r_long_range_B_refined7.442
r_dihedral_angle_1_deg6.509
r_scangle_other5.574
r_mcangle_it4.437
r_mcangle_other4.437
r_scbond_it3.429
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.057
r_dihedral_angle_4_deg19.096
r_dihedral_angle_3_deg14.682
r_long_range_B_other7.453
r_long_range_B_refined7.442
r_dihedral_angle_1_deg6.509
r_scangle_other5.574
r_mcangle_it4.437
r_mcangle_other4.437
r_scbond_it3.429
r_scbond_other3.429
r_mcbond_it2.858
r_mcbond_other2.853
r_angle_refined_deg1.725
r_angle_other_deg1.003
r_chiral_restr0.098
r_bond_refined_d0.017
r_gen_planes_refined0.008
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 Atoms16871
Nucleic Acid Atoms
Solvent Atoms985
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing