2JDU

Mutant (G24N) 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
10.2 M AMMONIUM SULFATE,30% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.0439.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.627α = 90
b = 74.886β = 114.71
c = 53.466γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR2006-03-14MSINGLE 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
11.528.6999.70.0614.83.760074
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)
11.51.5499.70.363.33.7

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 1UZV1.548.5657022302499.60.1510.1490.193RANDOM12.31
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]
-0.440.21-0.080.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.361
r_dihedral_angle_4_deg17.535
r_dihedral_angle_3_deg10.438
r_dihedral_angle_1_deg6.714
r_scangle_it3.564
r_scbond_it2.376
r_mcangle_it1.726
r_angle_refined_deg1.58
r_mcbond_it1.082
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.361
r_dihedral_angle_4_deg17.535
r_dihedral_angle_3_deg10.438
r_dihedral_angle_1_deg6.714
r_scangle_it3.564
r_scbond_it2.376
r_mcangle_it1.726
r_angle_refined_deg1.58
r_mcbond_it1.082
r_nbtor_refined0.297
r_symmetry_vdw_refined0.248
r_nbd_refined0.22
r_xyhbond_nbd_refined0.168
r_symmetry_hbond_refined0.163
r_chiral_restr0.12
r_bond_refined_d0.016
r_gen_planes_refined0.008
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 Atoms3324
Nucleic Acid Atoms
Solvent Atoms535
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing