5LY7

Crystal structure of NagZ H174A mutant from Pseudomonas aeruginosa in complex with the inhibitor 2-acetamido-1,2-dideoxynojirimycin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherCrystallographic structure of NagZ from Pseudomonas aeruginosa

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629130% PEG 8000, 100 mM Sodium Cacodylate pH 6.0, 200 mM Sodium Acetate pH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.0941.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.14α = 90
b = 66.93β = 98.57
c = 74.06γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97925ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
13.173.2393.10.1820.1460.9294.22.210753219.14
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)
13.13.3192.70.4050.752.22.1

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 REPLACEMENTTHROUGHOUTCrystallographic structure of NagZ from Pseudomonas aeruginosa3.173.231017556592.670.220690.216840.2909RANDOM17.773
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]
4.291.53-2.99-1.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.473
r_scbond_it32.705
r_scbond_other32.692
r_scangle_other29.748
r_long_range_B_refined28.006
r_long_range_B_other28.006
r_mcbond_it22.072
r_mcbond_other21.995
r_mcangle_other21.059
r_mcangle_it21.026
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.473
r_scbond_it32.705
r_scbond_other32.692
r_scangle_other29.748
r_long_range_B_refined28.006
r_long_range_B_other28.006
r_mcbond_it22.072
r_mcbond_other21.995
r_mcangle_other21.059
r_mcangle_it21.026
r_dihedral_angle_3_deg16.196
r_dihedral_angle_4_deg10.978
r_dihedral_angle_1_deg6.051
r_angle_other_deg1.963
r_angle_refined_deg1.509
r_chiral_restr0.069
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.006
r_bond_other_d0.003
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 Atoms5082
Nucleic Acid Atoms
Solvent Atoms15
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing