5NQ3

'Porcine (Sus scrofa) Major Histocompatibility Complex, class I, with human beta2 micro globulin, presenting EFEDLTFLA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291JBS screen, condition A07: 30% MPD, 100 mM Na Citrate, pH 5.6, 200 mM Ammonium Acetate
Crystal Properties
Matthews coefficientSolvent content
2.2745.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.301α = 81.48
b = 59.696β = 67.62
c = 66.443γ = 68.6
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 6M2016-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.5761.44960.065.71.910524023
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)
11.571.6193.30.6651.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5QQ31.5761.4499669511395.610.219890.217720.26232RANDOM26.823
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]
-0.910.070.140.170.440.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.501
r_dihedral_angle_4_deg18.82
r_dihedral_angle_3_deg16.436
r_dihedral_angle_1_deg6.679
r_long_range_B_refined6.043
r_long_range_B_other5.885
r_scangle_other2.267
r_angle_refined_deg1.818
r_mcangle_it1.54
r_mcangle_other1.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.501
r_dihedral_angle_4_deg18.82
r_dihedral_angle_3_deg16.436
r_dihedral_angle_1_deg6.679
r_long_range_B_refined6.043
r_long_range_B_other5.885
r_scangle_other2.267
r_angle_refined_deg1.818
r_mcangle_it1.54
r_mcangle_other1.54
r_scbond_it1.474
r_scbond_other1.47
r_angle_other_deg1.058
r_mcbond_it0.969
r_mcbond_other0.969
r_chiral_restr0.12
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6290
Nucleic Acid Atoms
Solvent Atoms795
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing