6R5N

The crystal structure of Glycoside Hydrolase BglX from P. aeruginosa in complex with 1-deoxynojirimycin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29150 mM Bis Tris, pH 6.5, 30% pentaerythritol ethoxylate and 50 mM ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.5852.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.942α = 90
b = 86.882β = 90
c = 244.18γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979310ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
1286.8897.20.116.88.9109537
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.030.58

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 REPLACEMENTTHROUGHOUT5TF0281.99103893554097.040.165940.164330.19606RANDOM21.568
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]
2.86-1.74-1.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.206
r_dihedral_angle_4_deg20.831
r_dihedral_angle_3_deg13.135
r_dihedral_angle_1_deg6.938
r_long_range_B_refined5.987
r_long_range_B_other5.746
r_scangle_other4.105
r_scbond_it2.589
r_scbond_other2.588
r_mcangle_it2.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.206
r_dihedral_angle_4_deg20.831
r_dihedral_angle_3_deg13.135
r_dihedral_angle_1_deg6.938
r_long_range_B_refined5.987
r_long_range_B_other5.746
r_scangle_other4.105
r_scbond_it2.589
r_scbond_other2.588
r_mcangle_it2.299
r_mcangle_other2.299
r_mcbond_it1.537
r_mcbond_other1.536
r_angle_refined_deg1.497
r_angle_other_deg1.378
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.007
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 Atoms11274
Nucleic Acid Atoms
Solvent Atoms1206
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing