1S7R

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
3.0359.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.192α = 90
b = 88.519β = 94
c = 120.026γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I7111.097MAX 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
12.952593.622159207412
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.953.189.1

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1N592.9524.842215919684104193.390.240.241650.239050.28961RANDOM23.203
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]
4.192.18-4.870.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.788
r_scangle_it2.704
r_scbond_it1.549
r_angle_refined_deg1.493
r_mcangle_it1.339
r_angle_other_deg0.902
r_mcbond_it0.702
r_symmetry_vdw_other0.278
r_symmetry_vdw_refined0.255
r_nbd_other0.247
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.788
r_scangle_it2.704
r_scbond_it1.549
r_angle_refined_deg1.493
r_mcangle_it1.339
r_angle_other_deg0.902
r_mcbond_it0.702
r_symmetry_vdw_other0.278
r_symmetry_vdw_refined0.255
r_nbd_other0.247
r_nbd_refined0.223
r_xyhbond_nbd_refined0.19
r_nbtor_other0.091
r_chiral_restr0.086
r_symmetry_hbond_refined0.037
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6276
Nucleic Acid Atoms
Solvent Atoms63
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing