4NSK

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72931.6-1.8 M AMMONIUM SULFATE, 0.1 M TRIS HCL PH 7.0-9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6553.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.46α = 90
b = 108.54β = 122.43
c = 57.39γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2007-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.826ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.5754.9940.16.92.4145341453450
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)
12.572.7188.20.5521.72.2

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1S7U2.619.09136361363672199.720.219250.219250.21590.28297RANDOM42.464
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]
0.060.03-0.090.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.33
r_dihedral_angle_4_deg20.013
r_dihedral_angle_3_deg19.642
r_dihedral_angle_1_deg7.198
r_scangle_it2.13
r_angle_refined_deg1.319
r_scbond_it1.227
r_mcangle_it1.134
r_angle_other_deg0.839
r_mcbond_it0.603
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.33
r_dihedral_angle_4_deg20.013
r_dihedral_angle_3_deg19.642
r_dihedral_angle_1_deg7.198
r_scangle_it2.13
r_angle_refined_deg1.319
r_scbond_it1.227
r_mcangle_it1.134
r_angle_other_deg0.839
r_mcbond_it0.603
r_chiral_restr0.078
r_mcbond_other0.07
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3142
Nucleic Acid Atoms
Solvent Atoms45
Heterogen Atoms

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling