6FCS

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OHU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29180mM Tris pH 8.5, 12% PEG 8000 and 160mM calcium acetate
Crystal Properties
Matthews coefficientSolvent content
3.1160.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 166.873α = 90
b = 166.873β = 90
c = 54.509γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97926ALBAXALOC

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
12.9144.5299.920.0929.919.919575
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.93

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 REPLACEMENTTHROUGHOUT5OHU2.9144.521859997299.930.196730.193050.26884RANDOM74.568
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]
-1.39-0.7-1.394.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.644
r_dihedral_angle_3_deg18.107
r_dihedral_angle_4_deg17.809
r_long_range_B_other7.312
r_long_range_B_refined7.311
r_dihedral_angle_1_deg5.858
r_scangle_other4.29
r_mcangle_other3.983
r_mcangle_it3.979
r_scbond_it2.481
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.644
r_dihedral_angle_3_deg18.107
r_dihedral_angle_4_deg17.809
r_long_range_B_other7.312
r_long_range_B_refined7.311
r_dihedral_angle_1_deg5.858
r_scangle_other4.29
r_mcangle_other3.983
r_mcangle_it3.979
r_scbond_it2.481
r_scbond_other2.481
r_mcbond_it2.412
r_mcbond_other2.392
r_angle_refined_deg1.361
r_angle_other_deg0.981
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.003
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 Atoms4972
Nucleic Acid Atoms
Solvent Atoms57
Heterogen Atoms180

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing