Experiment: 6H6D

 6H6D

Crystal structures of the murine class I major histocompatibility complex H-2Db in complex with adenovirus-derived peptide Ad10


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N5A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP92771.8M ammonium sulphate, 0.1M Tris
Crystal Properties
Matthews coefficientSolvent content
2.7455.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.14α = 84.2
b = 69.24β = 86.69
c = 87.16γ = 81.75
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2009-09-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-41.00ESRFID14-4

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
12.3420900.1378.53.542622
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)
12.342.50.64

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 REPLACEMENTTHROUGHOUT1N5A2.419.9838969200096.650.19990.198150.23333RANDOM48.314
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]
-0.090.110.040.270.32-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.885
r_dihedral_angle_4_deg21.845
r_dihedral_angle_3_deg18.428
r_long_range_B_other9.936
r_long_range_B_refined9.933
r_dihedral_angle_1_deg7.096
r_scangle_other7.035
r_mcangle_it6.163
r_mcangle_other6.163
r_scbond_it4.408
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6264
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing