1S7Q

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

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
3.0959.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.22α = 90
b = 135.871β = 90
c = 45.168γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-08-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I7110.97MAX 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
11.99141.4298.938269378482
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.992.194

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 1N591.9937.533826935920189498.790.182810.181420.20933RANDOM18.251
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]
0.040.18-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.621
r_scangle_it4.228
r_scbond_it2.544
r_mcangle_it1.605
r_angle_refined_deg1.488
r_angle_other_deg0.889
r_mcbond_it0.821
r_nbd_other0.255
r_symmetry_vdw_other0.227
r_nbd_refined0.202
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.621
r_scangle_it4.228
r_scbond_it2.544
r_mcangle_it1.605
r_angle_refined_deg1.488
r_angle_other_deg0.889
r_mcbond_it0.821
r_nbd_other0.255
r_symmetry_vdw_other0.227
r_nbd_refined0.202
r_symmetry_hbond_refined0.183
r_symmetry_vdw_refined0.174
r_xyhbond_nbd_refined0.172
r_chiral_restr0.11
r_nbtor_other0.085
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_gen_planes_other0.006
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3130
Nucleic Acid Atoms
Solvent Atoms258
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing