2JDN

Mutant (S22A) of Pseudomonas aeruginosa lectin II (PA-IIL) complexed with methyl-a-L-mannopyranoside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UZVPDB ENTRY 1UZV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5TRIS HCL 0.1M, PH8.5, 1.75 M AMMNONIUM SULFATE(THE PA-IIL/GLYCOMIMETIC COMPLEXE WAS OBTAINED BY SOAKING METHOD FROM FUCOSE-CONTAINING CRISTAL), pH 8.50
Crystal Properties
Matthews coefficientSolvent content
2.2244.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.49α = 90
b = 72.947β = 94.32
c = 54.653γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR2005-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.321.299.20.0423.14.299982
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)
11.31.3396.40.0812.43.8

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 1UZV1.354.4794963499399.20.1390.1380.155RANDOM10.28
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]
-0.4-0.050.130.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.266
r_dihedral_angle_4_deg21.251
r_dihedral_angle_3_deg10.848
r_dihedral_angle_1_deg6.837
r_scangle_it2.623
r_scbond_it1.844
r_angle_refined_deg1.42
r_mcangle_it1.322
r_mcbond_it0.796
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.266
r_dihedral_angle_4_deg21.251
r_dihedral_angle_3_deg10.848
r_dihedral_angle_1_deg6.837
r_scangle_it2.623
r_scbond_it1.844
r_angle_refined_deg1.42
r_mcangle_it1.322
r_mcbond_it0.796
r_nbtor_refined0.299
r_nbd_refined0.218
r_symmetry_vdw_refined0.16
r_symmetry_hbond_refined0.159
r_xyhbond_nbd_refined0.13
r_chiral_restr0.092
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms3304
Nucleic Acid Atoms
Solvent Atoms750
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing