2Q6W

The structure of HLA-DRA, DRB3*0101 (DR52a) with bound platelet integrin peptide associated with fetal and neonatal alloimmune thrombocytopenia


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.429710-20% PEG 8000, 0.1M sodium acetate, 10% (v/v) glycerol, 0.01M Cd2+, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K
Crystal Properties
Matthew coefficientSolvent content
2.9658.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.169α = 90
b = 92.169β = 90
c = 248.555γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98CCDADSC QUANTUM 42002-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.1NSLSX25

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
12.2530940.1215.851116480492242.9
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)
2.252.30855.70.363.04

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1DLH2.2520.0524777744561368493.270.2140.209840.26543RANDOM42.241
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]
0.820.82-1.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.671
r_dihedral_angle_4_deg22.268
r_dihedral_angle_3_deg18.375
r_dihedral_angle_1_deg8.266
r_scangle_it5.641
r_scbond_it3.834
r_mcangle_it2.551
r_angle_refined_deg2.478
r_mcbond_it1.677
r_nbtor_refined0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.671
r_dihedral_angle_4_deg22.268
r_dihedral_angle_3_deg18.375
r_dihedral_angle_1_deg8.266
r_scangle_it5.641
r_scbond_it3.834
r_mcangle_it2.551
r_angle_refined_deg2.478
r_mcbond_it1.677
r_nbtor_refined0.34
r_nbd_refined0.278
r_symmetry_hbond_refined0.267
r_symmetry_vdw_refined0.243
r_xyhbond_nbd_refined0.235
r_chiral_restr0.159
r_bond_refined_d0.029
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6043
Nucleic Acid Atoms
Solvent Atoms487
Heterogen Atoms

Software

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