2JDH

Lectin PA-IIL of P.aeruginosa complexed with disaccharide derivative


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)
Crystal Properties
Matthews coefficientSolvent content
2.2144.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.552α = 90
b = 72.829β = 94.29
c = 54.359γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR2006-01-24MSINGLE 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
11.122.2696.30.0522.65.2158737
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)
11.11.392.70.129.43.6

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 1UZV1.154.23153917479096.20.1080.1070.131RANDOM10.58
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]
-0.23-0.040.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.727
r_dihedral_angle_4_deg14.502
r_dihedral_angle_3_deg10.58
r_dihedral_angle_1_deg6.896
r_scangle_it4.628
r_scbond_it3.065
r_mcangle_it2.163
r_angle_refined_deg1.769
r_mcbond_it1.485
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.727
r_dihedral_angle_4_deg14.502
r_dihedral_angle_3_deg10.58
r_dihedral_angle_1_deg6.896
r_scangle_it4.628
r_scbond_it3.065
r_mcangle_it2.163
r_angle_refined_deg1.769
r_mcbond_it1.485
r_nbtor_refined0.302
r_nbd_refined0.233
r_symmetry_hbond_refined0.197
r_symmetry_vdw_refined0.193
r_xyhbond_nbd_refined0.144
r_chiral_restr0.131
r_bond_refined_d0.019
r_gen_planes_refined0.01
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 Atoms3308
Nucleic Acid Atoms
Solvent Atoms735
Heterogen Atoms117

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing