3TBY

CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX WITH THE LCMV-DERIVED GP33 ALTERED PEPTIDE ligand (V3P, Y4F)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293Crystals were obtained in 1.6-1.8 M ammonium sulfate, 0.1 M Tris HCl pH 7.0-9.0 screening conditions. 4 ul of a 5mg/ml protein solution were mixed in a 4:2 ratio with the crystallization reservoir , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.1260.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.82α = 90
b = 124.27β = 103.29
c = 99.65γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42008-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.93400ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.548.598.10.11210.73.7756937569355.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.6599.20.6311.911100

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 REPLACEMENTTHROUGHOUT1S7U2.5207060070600374997.90.286040.286040.284490.31473RANDOM38.631
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]
-0.12-0.870.1-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.045
r_dihedral_angle_4_deg23.293
r_dihedral_angle_3_deg17.503
r_dihedral_angle_1_deg6.345
r_scangle_it1.254
r_angle_refined_deg1.192
r_angle_other_deg0.817
r_scbond_it0.814
r_mcangle_it0.482
r_mcbond_it0.262
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.045
r_dihedral_angle_4_deg23.293
r_dihedral_angle_3_deg17.503
r_dihedral_angle_1_deg6.345
r_scangle_it1.254
r_angle_refined_deg1.192
r_angle_other_deg0.817
r_scbond_it0.814
r_mcangle_it0.482
r_mcbond_it0.262
r_mcbond_other0.076
r_chiral_restr0.075
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12264
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms

Software

Software
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling