2D3V

Crystal Structure of Leukocyte Ig-like Receptor A5 (LILRA5/LIR9/ILT11)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9293Bicine, PEG20000, Dioxane, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.549.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 28.08α = 90
b = 58.645β = 90
c = 131.619γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.97921, 0.97956, 0.90000, 1.0000SPring-8BL41XU

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
11.85092.10.05216.66.3193281
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)
1.81.8649.20.3822.53.41011

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.85501764595195.620.235470.233630.26861RANDOM34.844
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]
-1.170.40.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.144
r_dihedral_angle_3_deg18.481
r_dihedral_angle_4_deg16.864
r_dihedral_angle_1_deg7.272
r_scangle_it3.493
r_scbond_it2.307
r_mcangle_it1.701
r_angle_refined_deg1.551
r_mcbond_it1.046
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.144
r_dihedral_angle_3_deg18.481
r_dihedral_angle_4_deg16.864
r_dihedral_angle_1_deg7.272
r_scangle_it3.493
r_scbond_it2.307
r_mcangle_it1.701
r_angle_refined_deg1.551
r_mcbond_it1.046
r_nbtor_refined0.307
r_nbd_refined0.2
r_xyhbond_nbd_refined0.17
r_symmetry_vdw_refined0.169
r_symmetry_hbond_refined0.167
r_chiral_restr0.102
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms1436
Nucleic Acid Atoms
Solvent Atoms105
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing