5MB1

STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PA14 IN COMPLEX WITH 2,4,6-Trimethylphenylsulfonamide-N-methyl-L-fucopyranoside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A6Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.529220% peg 6K 0.5M LiCl 0.1 M citric acid Ph 4.5
Crystal Properties
Matthews coefficientSolvent content
2.0640.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.904α = 90
b = 65.251β = 90
c = 108.987γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.9205ESRFBM30A

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
11.6541.8398.80.0560.99819.14.34557229.8
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)
11.651.6899.60.30.9024.54.3

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 REPLACEMENTTHROUGHOUT5a6q1.6541.8343249227198.60.132940.131760.15505RANDOM9.171
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]
0.53-0.46-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg47.903
r_dihedral_angle_4_deg17.6
r_dihedral_angle_3_deg10.814
r_dihedral_angle_1_deg6.581
r_long_range_B_refined4.303
r_long_range_B_other3.831
r_scangle_other2.103
r_angle_refined_deg1.733
r_scbond_it1.403
r_scbond_other1.399
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg47.903
r_dihedral_angle_4_deg17.6
r_dihedral_angle_3_deg10.814
r_dihedral_angle_1_deg6.581
r_long_range_B_refined4.303
r_long_range_B_other3.831
r_scangle_other2.103
r_angle_refined_deg1.733
r_scbond_it1.403
r_scbond_other1.399
r_mcangle_it1.247
r_mcangle_other1.247
r_angle_other_deg0.993
r_mcbond_it0.76
r_mcbond_other0.755
r_chiral_restr0.112
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
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 Atoms3280
Nucleic Acid Atoms
Solvent Atoms655
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing