2WRA

BclA lectin from Burkholderia cenocepacia complexed with aMan1(aMan1- 6)-3Man trisaccharide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VNVPDB ENTRY 2VNV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
180% OF THE INITIAL PRECIPITANT SOLUTION (30% PEG IN 0.2M AMMONIUM SULPHATE)
Crystal Properties
Matthews coefficientSolvent content
2.1342.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.296α = 90
b = 66.296β = 90
c = 46.159γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMIRRORS2006-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.157.4596.50.0516.84477042.4
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)
11.11.1679.80.222.42

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 2VNV1.157.4543671230396.380.144990.143550.173RANDOM10.224
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]
0.120.060.12-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.935
r_dihedral_angle_4_deg13.552
r_dihedral_angle_3_deg11.61
r_sphericity_free9.616
r_dihedral_angle_1_deg8.018
r_scangle_it4.56
r_sphericity_bonded4.126
r_scbond_it3.379
r_mcangle_it2.851
r_angle_refined_deg2.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.935
r_dihedral_angle_4_deg13.552
r_dihedral_angle_3_deg11.61
r_sphericity_free9.616
r_dihedral_angle_1_deg8.018
r_scangle_it4.56
r_sphericity_bonded4.126
r_scbond_it3.379
r_mcangle_it2.851
r_angle_refined_deg2.01
r_mcbond_it1.902
r_rigid_bond_restr1.655
r_angle_other_deg1.551
r_mcbond_other0.816
r_chiral_restr0.134
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms932
Nucleic Acid Atoms
Solvent Atoms178
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing