2JDM

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.50.2 M LITHIUM MONOHYDRATE SULFATE,0.1 M TRIS HYDROCLORIDE (PH 8.5), 30% PEG 4000, (PA-IIL/A-L-ME-FUC COMPLEX WAS OBTAINED BY SOAKING METHOD FROM FUCOSE-CONTAINING CRISTAL)
Crystal Properties
Matthews coefficientSolvent content
2.2545.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.674α = 90
b = 73.09β = 94.25
c = 54.917γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR2006-02-26MSINGLE 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
11.734.6795.40.0814.43.743407
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)
11.71.7492.40.323.53.6

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 1UZV1.754.841187220094.90.1770.1740.223RANDOM11.29
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]
-0.67-0.190.420.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.893
r_dihedral_angle_4_deg22.871
r_dihedral_angle_3_deg11.235
r_dihedral_angle_1_deg6.457
r_scangle_it2.68
r_scbond_it1.795
r_angle_refined_deg1.289
r_mcangle_it1.081
r_mcbond_it0.649
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.893
r_dihedral_angle_4_deg22.871
r_dihedral_angle_3_deg11.235
r_dihedral_angle_1_deg6.457
r_scangle_it2.68
r_scbond_it1.795
r_angle_refined_deg1.289
r_mcangle_it1.081
r_mcbond_it0.649
r_nbtor_refined0.297
r_nbd_refined0.217
r_symmetry_vdw_refined0.19
r_symmetry_hbond_refined0.147
r_xyhbond_nbd_refined0.128
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.005
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 Atoms524
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing