6GXR

Crystal structure of BP39L lectin from Burkholderia pseudomallei at 1.7 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52900.1 M MES, 15% PEG 5000 MME, 0.2 M ammonium sulphate, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
1.9336.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.076α = 90
b = 87.549β = 90
c = 159.1γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2013-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.979PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.779.5594.70.071125.11433933
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7995.90.430.9246.214.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.779.5532232170194.450.15930.157370.19609RANDOM16.887
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]
0.334.57-4.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.394
r_dihedral_angle_4_deg16.741
r_dihedral_angle_3_deg12.667
r_dihedral_angle_1_deg7.79
r_long_range_B_refined5.784
r_long_range_B_other5.655
r_scangle_other4.063
r_scbond_it2.694
r_scbond_other2.682
r_mcangle_it2.523
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.394
r_dihedral_angle_4_deg16.741
r_dihedral_angle_3_deg12.667
r_dihedral_angle_1_deg7.79
r_long_range_B_refined5.784
r_long_range_B_other5.655
r_scangle_other4.063
r_scbond_it2.694
r_scbond_other2.682
r_mcangle_it2.523
r_mcangle_other2.522
r_angle_refined_deg2.099
r_mcbond_it1.812
r_mcbond_other1.81
r_angle_other_deg1.108
r_chiral_restr0.139
r_bond_refined_d0.023
r_gen_planes_refined0.013
r_bond_other_d0.007
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2596
Nucleic Acid Atoms
Solvent Atoms317
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing