1W8F

PSEUDOMONAS AERUGINOSA LECTIN II (PA-IIL)COMPLEXED WITH LACTO-N-NEO- FUCOPENTAOSE V(LNPFV)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GZTPDB ENTRY 1GZT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5TRIS HCL 0.1M, PH8.5, 1.75 M AMMNONIUM SULFATE, pH 8.50
Crystal Properties
Matthews coefficientSolvent content
2.345.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.015α = 85.35
b = 48.352β = 80.05
c = 52.472γ = 65.6
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMULTILAYER MIRROR2004-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.0514.5193.30.0774.1180957
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)
11.051.0889.50.321.83.5

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 1GZT1.0514.51171406907293.30.1060.1050.123RANDOM7.31
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.259
r_scangle_it4.905
r_scbond_it3.522
r_mcangle_it2.849
r_angle_refined_deg2.059
r_mcbond_it2.018
r_angle_other_deg1.292
r_symmetry_vdw_other0.348
r_nbd_other0.275
r_xyhbond_nbd_refined0.275
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.259
r_scangle_it4.905
r_scbond_it3.522
r_mcangle_it2.849
r_angle_refined_deg2.059
r_mcbond_it2.018
r_angle_other_deg1.292
r_symmetry_vdw_other0.348
r_nbd_other0.275
r_xyhbond_nbd_refined0.275
r_nbd_refined0.247
r_symmetry_hbond_refined0.229
r_symmetry_vdw_refined0.169
r_chiral_restr0.156
r_nbtor_other0.094
r_bond_refined_d0.021
r_gen_planes_refined0.017
r_bond_other_d0.003
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms727
Heterogen Atoms236

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
ACORNphasing