6FC4

The X-ray Structure of Lytic Transglycosylase Slt inactive mutant E503Q from Pseudomonas aeruginosa


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
3.0759.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 163.488α = 90
b = 163.488β = 90
c = 56.035γ = 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
13.05141.5899.880.04811.9411.716595
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)
13.053.160.39

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 REPLACEMENTTHROUGHOUT5OHU3.05141.581578581099.90.184680.181460.24967RANDOM82.949
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]
0.70.350.7-2.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.794
r_dihedral_angle_4_deg18.657
r_dihedral_angle_3_deg17.193
r_long_range_B_refined6.699
r_long_range_B_other6.698
r_dihedral_angle_1_deg6.016
r_mcangle_it4.264
r_mcangle_other4.263
r_scangle_other4.124
r_mcbond_it2.559
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.794
r_dihedral_angle_4_deg18.657
r_dihedral_angle_3_deg17.193
r_long_range_B_refined6.699
r_long_range_B_other6.698
r_dihedral_angle_1_deg6.016
r_mcangle_it4.264
r_mcangle_other4.263
r_scangle_other4.124
r_mcbond_it2.559
r_mcbond_other2.557
r_scbond_it2.38
r_scbond_other2.379
r_angle_refined_deg1.206
r_angle_other_deg0.931
r_chiral_restr0.066
r_bond_refined_d0.007
r_gen_planes_refined0.004
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 Atoms4980
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing