1S7S

Crystal structures of the murine class I major histocompatibility complex H-2Kb in complex with LCMV-derived gp33 index peptide and three of its escape variants


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N59PDB entry 1N59

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293sodium/potassium phosphate, Methyl pentane diol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0859.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.262α = 90
b = 135.555β = 90
c = 45.13γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM141.069ESRFBM14

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
11.995092.939141363622
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.992.180.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1N591.9919.883914133520175092.860.192060.190010.23191RANDOM21.868
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]
0.030.11-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.796
r_scangle_it4.304
r_scbond_it2.641
r_angle_refined_deg1.694
r_mcangle_it1.601
r_angle_other_deg0.936
r_mcbond_it0.859
r_symmetry_vdw_other0.268
r_nbd_other0.261
r_nbd_refined0.214
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.796
r_scangle_it4.304
r_scbond_it2.641
r_angle_refined_deg1.694
r_mcangle_it1.601
r_angle_other_deg0.936
r_mcbond_it0.859
r_symmetry_vdw_other0.268
r_nbd_other0.261
r_nbd_refined0.214
r_xyhbond_nbd_refined0.191
r_symmetry_hbond_refined0.184
r_symmetry_vdw_refined0.123
r_chiral_restr0.112
r_nbtor_other0.09
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3131
Nucleic Acid Atoms
Solvent Atoms268
Heterogen Atoms

Software

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