1ZT7

crystal structure of class I MHC H-2Kk in complex with a nonapeptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52931.6M ammonium sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.8357

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.135α = 90
b = 72.628β = 111.24
c = 88.793γ = 90
Symmetry
Space GroupP 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-06-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.93300ESRFID14-2

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
132090.20.1582.5183021154.3
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)
33.0590.40.3972.4937

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTthe complex between H-2Kk and the octapeptide HA(259-266)3151733086689.680.234740.234740.230940.31074RANDOM4.551
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]
20.681.28-2.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.074
r_angle_refined_deg1.21
r_scangle_it1.069
r_angle_other_deg0.835
r_scbond_it0.646
r_mcangle_it0.359
r_symmetry_vdw_refined0.29
r_symmetry_vdw_other0.221
r_nbd_other0.207
r_xyhbond_nbd_refined0.202
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.074
r_angle_refined_deg1.21
r_scangle_it1.069
r_angle_other_deg0.835
r_scbond_it0.646
r_mcangle_it0.359
r_symmetry_vdw_refined0.29
r_symmetry_vdw_other0.221
r_nbd_other0.207
r_xyhbond_nbd_refined0.202
r_nbd_refined0.198
r_mcbond_it0.185
r_symmetry_hbond_refined0.092
r_nbtor_other0.085
r_chiral_restr0.073
r_bond_refined_d0.01
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6334
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing