3E6J

Crystal Structure of Variable Lymphocyte Receptor (VLR) RBC36 in Complex with H-trisaccharide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2R9UPDB ENTRY 2R9U

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62951.9 M (NH4)2SO4, 0.1 M Sodium Citrate (pH 5.6), 0.2 M K/Na Tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.5952.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.221α = 90
b = 48.564β = 116.51
c = 55.477γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)2008-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.98SSRLBL11-1

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
11.675095.30.08913.83.63008028666-3
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)
11.671.7171.10.2283.72.72120

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 2R9U1.6749.632861327202145495.070.148250.14640.18221RANDOM11.524
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]
1.63-0.08-0.97-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.511
r_dihedral_angle_4_deg20.817
r_dihedral_angle_3_deg10.696
r_dihedral_angle_1_deg6.131
r_scangle_it5.569
r_scbond_it3.648
r_mcangle_it2.131
r_angle_refined_deg1.62
r_angle_other_deg1.548
r_mcbond_it1.186
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.511
r_dihedral_angle_4_deg20.817
r_dihedral_angle_3_deg10.696
r_dihedral_angle_1_deg6.131
r_scangle_it5.569
r_scbond_it3.648
r_mcangle_it2.131
r_angle_refined_deg1.62
r_angle_other_deg1.548
r_mcbond_it1.186
r_mcbond_other0.271
r_chiral_restr0.197
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1678
Nucleic Acid Atoms
Solvent Atoms330
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing