2BOJ

crystal Structure of pseudomonas aeruginosa lectin (PA-IIL) complexed with methyl-B-D-Arabinopyranoside


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 AMMONIUM SULFATE, pH 8.50
Crystal Properties
Matthews coefficientSolvent content
1.7429

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.636α = 90
b = 80.168β = 109.92
c = 52.517γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR2002-06-10MSINGLE 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
11.829.697.90.077.53.7335769
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)
11.81.9890.193.643.45

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 1UZV1.849.3934653111697.70.1370.1360.172RANDOM11.43
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]
-0.050.01-0.030.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.637
r_dihedral_angle_4_deg19.172
r_dihedral_angle_3_deg11.568
r_dihedral_angle_1_deg6.521
r_scangle_it2.832
r_scbond_it1.751
r_angle_refined_deg1.32
r_mcangle_it1.051
r_mcbond_it0.621
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.637
r_dihedral_angle_4_deg19.172
r_dihedral_angle_3_deg11.568
r_dihedral_angle_1_deg6.521
r_scangle_it2.832
r_scbond_it1.751
r_angle_refined_deg1.32
r_mcangle_it1.051
r_mcbond_it0.621
r_nbtor_refined0.301
r_nbd_refined0.222
r_symmetry_vdw_refined0.193
r_symmetry_hbond_refined0.183
r_xyhbond_nbd_refined0.154
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 Atoms3308
Nucleic Acid Atoms
Solvent Atoms612
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing