6FI2 | pdb_00006fi2

VexL: A periplasmic depolymerase provides new insight into ABC transporter-dependent secretion of bacterial capsular polysaccharides


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52931.58 M sodium malonate, 0.1 M BisTris HCl pH 6.5, 0.13 M ammonium citrate, and 2.5 % (v/v) 2-methyl-2,4-pentanediol
Crystal Properties
Matthews coefficientSolvent content
2.0540

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.68α = 90
b = 94.68β = 90
c = 78.84γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-FToroidal mirror2017-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.972422ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.2260.61001712.8106029
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.221.241000.7782.112.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.2260.6100829520099.950.140380.139050.13920.166210.1663RANDOM19.66
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]
-1.16-1.162.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.039
r_sphericity_free22.198
r_dihedral_angle_4_deg14.286
r_dihedral_angle_3_deg11.64
r_sphericity_bonded9.106
r_dihedral_angle_1_deg6.921
r_long_range_B_refined3.003
r_long_range_B_other3.001
r_scangle_other2.646
r_rigid_bond_restr2.277
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.039
r_sphericity_free22.198
r_dihedral_angle_4_deg14.286
r_dihedral_angle_3_deg11.64
r_sphericity_bonded9.106
r_dihedral_angle_1_deg6.921
r_long_range_B_refined3.003
r_long_range_B_other3.001
r_scangle_other2.646
r_rigid_bond_restr2.277
r_scbond_it2.192
r_scbond_other2.192
r_mcangle_it2.004
r_mcangle_other2.003
r_angle_refined_deg1.561
r_mcbond_it1.524
r_mcbond_other1.519
r_angle_other_deg0.991
r_chiral_restr0.102
r_bond_refined_d0.012
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2942
Nucleic Acid Atoms
Solvent Atoms243
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata scaling
BALBESphasing
XDSdata reduction