6FCU

The X-ray Structure of Lytic Transglycosylase Slt inactive mutant E503Q from Pseudomonas aeruginosa in complex with 4(NAG-NAMpentapeptide)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29180mM Tris pH 8.5, 12% PEG 8000 and 160mM calcium acetate
Crystal Properties
Matthew coefficientSolvent content
3.0159.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 164.293α = 90
b = 164.293β = 90
c = 55.954γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97953ALBAXALOC

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
13.2142.2899.910.0619.359.414530
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.23.32

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 REPLACEMENTTHROUGHOUT5OHU3.2142.281384768199.930.196670.192920.27247RANDOM94.973
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]
10.51-3.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.796
r_dihedral_angle_3_deg18.289
r_dihedral_angle_4_deg18.186
r_long_range_B_other9.041
r_long_range_B_refined9.041
r_dihedral_angle_1_deg6.61
r_mcangle_other6.18
r_mcangle_it6.18
r_scangle_other5.634
r_mcbond_it3.747
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.796
r_dihedral_angle_3_deg18.289
r_dihedral_angle_4_deg18.186
r_long_range_B_other9.041
r_long_range_B_refined9.041
r_dihedral_angle_1_deg6.61
r_mcangle_other6.18
r_mcangle_it6.18
r_scangle_other5.634
r_mcbond_it3.747
r_mcbond_other3.745
r_scbond_it3.277
r_scbond_other3.276
r_angle_refined_deg1.416
r_angle_other_deg1
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.002
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5113
Nucleic Acid Atoms
Solvent Atoms57
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing