2JDP

Mutant (S23A) 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
17.50.2 M DIGYDRATED CALCIUM CHLORIDE, 0.1 M TRIHYDRATED SODIUM ACETATE (PH7.5), 20% ISO-PROPANOL, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.0339.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.062α = 90
b = 45.69β = 94.21
c = 87.952γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR2006-04-07MSINGLE 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
11.387.7195.80.0516.23.398919
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)
11.31.33930.352.63.2

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 1UZV1.387.7184498442195.90.1710.1690.197RANDOM12.86
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]
-0.42-0.290.41-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.44
r_dihedral_angle_4_deg22.368
r_dihedral_angle_3_deg10.575
r_dihedral_angle_1_deg6.646
r_scangle_it2.767
r_scbond_it1.823
r_angle_refined_deg1.476
r_mcangle_it1.441
r_mcbond_it0.946
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.44
r_dihedral_angle_4_deg22.368
r_dihedral_angle_3_deg10.575
r_dihedral_angle_1_deg6.646
r_scangle_it2.767
r_scbond_it1.823
r_angle_refined_deg1.476
r_mcangle_it1.441
r_mcbond_it0.946
r_nbtor_refined0.301
r_nbd_refined0.217
r_symmetry_vdw_refined0.211
r_symmetry_hbond_refined0.152
r_xyhbond_nbd_refined0.139
r_chiral_restr0.102
r_bond_refined_d0.013
r_gen_planes_refined0.007
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 Atoms592
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing