5AJC

X-ray structure of RSL lectin in complex with sialyl lewis X tetrasaccharide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.530% PEG 6K 280MM TRIS PH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.3146.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.766α = 90
b = 83.163β = 90
c = 90.697γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2013-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
11.731.5399.10.0514.53.5310532
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)
11.71.7399.90.343.13.5

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 2BT91.734.0729519149898.670.152570.150830.18673RANDOM15.412
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]
-0.99-0.911.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.962
r_dihedral_angle_3_deg11.18
r_dihedral_angle_1_deg6.815
r_dihedral_angle_4_deg6.541
r_angle_other_deg2.325
r_mcangle_it2.224
r_angle_refined_deg1.716
r_scbond_it1.663
r_mcbond_it1.369
r_mcbond_other1.369
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.962
r_dihedral_angle_3_deg11.18
r_dihedral_angle_1_deg6.815
r_dihedral_angle_4_deg6.541
r_angle_other_deg2.325
r_mcangle_it2.224
r_angle_refined_deg1.716
r_scbond_it1.663
r_mcbond_it1.369
r_mcbond_other1.369
r_chiral_restr0.1
r_bond_refined_d0.015
r_bond_other_d0.012
r_gen_planes_refined0.011
r_gen_planes_other0.008
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 Atoms2023
Nucleic Acid Atoms
Solvent Atoms362
Heterogen Atoms180

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing