1S7V

Crystal structures of the murine class I major histocompatibility complex H-2Db 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 1N5APDB entry 1N5A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293Ammonium sulfate, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.1860.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 160.469α = 90
b = 91.184β = 125
c = 92.147γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARRESEARCH2003-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.979ESRFID29

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
12.23294.455257521632
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.22.25794.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 1N5A2.232.4425525749523263994.410.227610.22560.26678RANDOM19.852
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]
2.261.621.72-2.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.953
r_scangle_it2.661
r_scbond_it1.671
r_angle_refined_deg1.401
r_mcangle_it1.145
r_angle_other_deg0.924
r_mcbond_it0.634
r_symmetry_hbond_refined0.358
r_symmetry_vdw_other0.271
r_nbd_other0.262
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.953
r_scangle_it2.661
r_scbond_it1.671
r_angle_refined_deg1.401
r_mcangle_it1.145
r_angle_other_deg0.924
r_mcbond_it0.634
r_symmetry_hbond_refined0.358
r_symmetry_vdw_other0.271
r_nbd_other0.262
r_xyhbond_nbd_refined0.235
r_nbd_refined0.233
r_symmetry_vdw_refined0.125
r_nbtor_other0.09
r_chiral_restr0.087
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6207
Nucleic Acid Atoms
Solvent Atoms444
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing