2GW5

Crystal Structure of LIR-2 (ILT4) at 1.8 : differences from LIR-1 (ILT2) in regions implicated in the binding of the Cytomegalovirus class I MHC homolog UL18


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1G0XPDB entry 1G0X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.50.1M Hepes pH 7.5, 10% Isopropanol, 20% PEG 4000 streak seeded., VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.3848.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.53α = 90
b = 62.53β = 90
c = 106.917γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.999SSRLBL9-2

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
11.834.199.3202901924111
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.83100

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 1G0X1.834.081923999199.380.24230.240410.27864RANDOM28.611
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.96
r_dihedral_angle_4_deg20.317
r_dihedral_angle_3_deg16.954
r_dihedral_angle_1_deg7.262
r_scangle_it5.362
r_scbond_it3.865
r_mcangle_it2.451
r_angle_refined_deg2.162
r_mcbond_it1.623
r_symmetry_hbond_refined0.368
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.96
r_dihedral_angle_4_deg20.317
r_dihedral_angle_3_deg16.954
r_dihedral_angle_1_deg7.262
r_scangle_it5.362
r_scbond_it3.865
r_mcangle_it2.451
r_angle_refined_deg2.162
r_mcbond_it1.623
r_symmetry_hbond_refined0.368
r_nbtor_refined0.319
r_nbd_refined0.314
r_symmetry_vdw_refined0.3
r_xyhbond_nbd_refined0.206
r_chiral_restr0.161
r_bond_refined_d0.026
r_gen_planes_refined0.01
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 Atoms1398
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
SCALEPACKdata scaling
AMoREphasing