3ZWE | pdb_00003zwe

Structure of BambL, a lectin from Burkholderia ambifaria, complexed with blood group B epitope


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WZ0PDB ENTRY 3WZ0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.0640.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.98α = 90
b = 49.14β = 90
c = 102.71γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2010-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30AESRFBM30A

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
11.7549.14960.05133.324165321.315
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)
11.751.8479.90.352.22.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3WZ01.7544.3322870121895.520.210950.207970.210.265790.26RANDOM25.215
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]
-0.55-1.371.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.604
r_dihedral_angle_3_deg14.616
r_dihedral_angle_1_deg6.74
r_dihedral_angle_4_deg5.826
r_scangle_it3.039
r_scbond_it2.194
r_mcangle_it1.836
r_angle_refined_deg1.622
r_xyhbond_nbd_refined1.086
r_mcbond_it1.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.604
r_dihedral_angle_3_deg14.616
r_dihedral_angle_1_deg6.74
r_dihedral_angle_4_deg5.826
r_scangle_it3.039
r_scbond_it2.194
r_mcangle_it1.836
r_angle_refined_deg1.622
r_xyhbond_nbd_refined1.086
r_mcbond_it1.084
r_nbtor_refined0.312
r_nbd_refined0.205
r_symmetry_vdw_refined0.204
r_symmetry_hbond_refined0.161
r_chiral_restr0.11
r_bond_refined_d0.016
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 Atoms1983
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms143

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing