5ENP

MBX2931 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
2.7354.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.646α = 90
b = 145.336β = 90
c = 174.218γ = 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
11.95099.60.1160.9979.348.1216569
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)
11.92.0198.11.4380.467.9

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 REPLACEMENTTHROUGHOUT5en51.9502057911065899.950.183670.181730.22154RANDOM34.938
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]
1.21-0.62-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.726
r_dihedral_angle_4_deg17.823
r_dihedral_angle_3_deg13.259
r_long_range_B_other8
r_long_range_B_refined7.992
r_scangle_other6.474
r_dihedral_angle_1_deg6.29
r_mcangle_it4.37
r_mcangle_other4.37
r_scbond_it4.198
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.726
r_dihedral_angle_4_deg17.823
r_dihedral_angle_3_deg13.259
r_long_range_B_other8
r_long_range_B_refined7.992
r_scangle_other6.474
r_dihedral_angle_1_deg6.29
r_mcangle_it4.37
r_mcangle_other4.37
r_scbond_it4.198
r_scbond_other4.198
r_mcbond_it3.123
r_mcbond_other3.122
r_angle_refined_deg1.822
r_angle_other_deg1.022
r_chiral_restr0.112
r_bond_refined_d0.018
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 Atoms16866
Nucleic Acid Atoms
Solvent Atoms1282
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing