1S7T

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
358.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.298α = 90
b = 92.688β = 90
c = 128.443γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I7111.007MAX III711

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
12.295098.847923473482
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.292.4292.2

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 1N592.319.884792345308191599.210.206520.204670.25193RANDOM27.089
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]
-0.050.06-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.459
r_scangle_it2.652
r_scbond_it1.525
r_angle_refined_deg1.195
r_mcangle_it1.07
r_angle_other_deg0.805
r_mcbond_it0.547
r_nbd_other0.236
r_xyhbond_nbd_refined0.212
r_nbd_refined0.189
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.459
r_scangle_it2.652
r_scbond_it1.525
r_angle_refined_deg1.195
r_mcangle_it1.07
r_angle_other_deg0.805
r_mcbond_it0.547
r_nbd_other0.236
r_xyhbond_nbd_refined0.212
r_nbd_refined0.189
r_symmetry_hbond_refined0.154
r_symmetry_vdw_other0.152
r_symmetry_vdw_refined0.102
r_nbtor_other0.084
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.004
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6258
Nucleic Acid Atoms
Solvent Atoms363
Heterogen Atoms

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4data scaling