6G9R

Murine class I major histocompatibility complex H-2 Db in complex with self-antigen derived from dopamine monooxygenase.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82931.5-2.0M ammonium sulfate 0.1M TRIS HCL, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
3.0759.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.245α = 90
b = 123.597β = 103.07
c = 99.262γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2011-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.072ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.75094.50.0590.0590.9988.22.413570956263
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.7795.90.4270.641.5

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 REPLACEMENTTHROUGHOUT1s7u2.74553380284394.30.235620.234070.26441RANDOM82.239
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]
-2.011.792.57-1.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.492
r_dihedral_angle_4_deg23.028
r_dihedral_angle_3_deg20.61
r_long_range_B_refined13.714
r_long_range_B_other13.714
r_mcangle_it10.213
r_mcangle_other10.213
r_scangle_other9.889
r_dihedral_angle_1_deg7.347
r_mcbond_it6.515
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.492
r_dihedral_angle_4_deg23.028
r_dihedral_angle_3_deg20.61
r_long_range_B_refined13.714
r_long_range_B_other13.714
r_mcangle_it10.213
r_mcangle_other10.213
r_scangle_other9.889
r_dihedral_angle_1_deg7.347
r_mcbond_it6.515
r_mcbond_other6.515
r_scbond_it6.253
r_scbond_other6.252
r_angle_refined_deg1.522
r_angle_other_deg1.109
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.005
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 Atoms12632
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing