1OF2

Crystal structure of HLA-B*2709 complexed with the vasoactive intestinal peptide type 1 receptor (VIPR) peptide (residues 400-408)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K5NPDB ENTRY 1K5N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5291TRIS PH 8.5, 19% PEG 8000 HANGING DROP, TEMPERATURE 291K
Crystal Properties
Matthews coefficientSolvent content
2.957

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.158α = 90
b = 81.635β = 107.47
c = 65.31γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2002-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.229.1960.129.73.125005
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.28970.354.13

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 1K5N2.262.0223736126795.80.1910.1880.244RANDOM33.81
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]
-0.041.170.010.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.788
r_scangle_it2.842
r_scbond_it1.711
r_angle_refined_deg1.259
r_mcangle_it1.117
r_angle_other_deg0.815
r_mcbond_it0.611
r_symmetry_vdw_other0.295
r_nbd_other0.245
r_nbd_refined0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.788
r_scangle_it2.842
r_scbond_it1.711
r_angle_refined_deg1.259
r_mcangle_it1.117
r_angle_other_deg0.815
r_mcbond_it0.611
r_symmetry_vdw_other0.295
r_nbd_other0.245
r_nbd_refined0.18
r_xyhbond_nbd_refined0.178
r_symmetry_hbond_refined0.167
r_symmetry_vdw_refined0.109
r_chiral_restr0.081
r_nbtor_other0.08
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_gen_planes_other0.003
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3191
Nucleic Acid Atoms
Solvent Atoms342
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing