5A6X

Structure of the LecB lectin from Pseudomonas aeruginosa strain PA14 in complex with alpha-methyl-fucoside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A6QPDB ENTRY 5A6Q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
13.826% PEG 8K 1M LICL 0.1M CITRIC ACID PH 3.8
Crystal Properties
Matthews coefficientSolvent content
2.0239.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.558α = 90
b = 65.585β = 90
c = 109.036γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30AESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.5537.8499.90.0720.96.4554702
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.5898.50.393.44.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 5A6Q1.5537.8452637276399.870.129440.128180.1534RANDOM9.03
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]
0.47-0.15-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg46.241
r_dihedral_angle_3_deg9.598
r_dihedral_angle_1_deg6.844
r_dihedral_angle_4_deg4.461
r_angle_other_deg2.004
r_angle_refined_deg1.641
r_scbond_it1.252
r_mcangle_it1.1
r_mcbond_it0.694
r_mcbond_other0.694
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg46.241
r_dihedral_angle_3_deg9.598
r_dihedral_angle_1_deg6.844
r_dihedral_angle_4_deg4.461
r_angle_other_deg2.004
r_angle_refined_deg1.641
r_scbond_it1.252
r_mcangle_it1.1
r_mcbond_it0.694
r_mcbond_other0.694
r_chiral_restr0.1
r_bond_refined_d0.015
r_bond_other_d0.012
r_gen_planes_refined0.009
r_gen_planes_other0.009
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3280
Nucleic Acid Atoms
Solvent Atoms759
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing