4K5U

Recognition of the BG-H Antigen by a Lamprey Variable Lymphocyte Receptor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729828.5% (w/v) PEG 3350, 0.6 M NaCl, and 0.1M Tris-HCl (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1643.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.71α = 72.03
b = 62.784β = 71.39
c = 63.366γ = 84.35
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2012-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.69859.7293.38859882662
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.6981.7687.8

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3E6J1.69859.728859882662415493.380.207720.205660.205660.24661RANDOM22.4
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]
-0.240.24-0.050.58-0.35-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.661
r_dihedral_angle_4_deg19.589
r_dihedral_angle_3_deg12.827
r_dihedral_angle_1_deg6.675
r_scangle_it6.276
r_scbond_it4.004
r_mcangle_it2.558
r_angle_refined_deg2.22
r_mcbond_it1.482
r_chiral_restr0.165
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.661
r_dihedral_angle_4_deg19.589
r_dihedral_angle_3_deg12.827
r_dihedral_angle_1_deg6.675
r_scangle_it6.276
r_scbond_it4.004
r_mcangle_it2.558
r_angle_refined_deg2.22
r_mcbond_it1.482
r_chiral_restr0.165
r_bond_refined_d0.028
r_gen_planes_refined0.014
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6642
Nucleic Acid Atoms
Solvent Atoms384
Heterogen Atoms48

Software

Software
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling