5AJB

X-ray structure of the RSL lectin in complex with Lewis X tetrasaccahride


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BT9PDB ENTRY 2BT9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.527% PEG 6K, 0.1 M TRIS, PH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.2344.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.185α = 90
b = 58.63β = 90
c = 106.713γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2012-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.840.0399.40.0816.15.3256062
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)
11.81.8499.90.374.15.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2BT91.840.0324275130499.010.147430.145660.18021RANDOM11.752
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]
-0.52-0.51.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.294
r_dihedral_angle_3_deg10.564
r_dihedral_angle_1_deg7.019
r_dihedral_angle_4_deg7.003
r_angle_refined_deg1.87
r_angle_other_deg1.851
r_mcangle_it1.705
r_scbond_it1.571
r_mcbond_it1.021
r_mcbond_other1.015
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.294
r_dihedral_angle_3_deg10.564
r_dihedral_angle_1_deg7.019
r_dihedral_angle_4_deg7.003
r_angle_refined_deg1.87
r_angle_other_deg1.851
r_mcangle_it1.705
r_scbond_it1.571
r_mcbond_it1.021
r_mcbond_other1.015
r_chiral_restr0.105
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_bond_other_d0.01
r_gen_planes_other0.01
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_it
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 Atoms2035
Nucleic Acid Atoms
Solvent Atoms345
Heterogen Atoms212

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing