3CUP

Crystal structure of the MHC class II molecule I-Ag7 in complex with the peptide GAD221-235


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ES0PDB ENTRY 1ES0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.52950.1M Hepes pH 7.5, 28% PEG 8000, 2% Jeffamine 900, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.856.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.832α = 90
b = 55.832β = 90
c = 338.834γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray96CCDADSC QUANTUM 41999-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.9795SSRLBL9-2

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
13.08838.44998.70.12810.64.910586-360.07
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.1599.40.6821.84.7

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1ES03.0938.45107291058656398.70.2350.2320.286RANDOM73.44
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]
5.3615.361-25.103
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.721
f_angle_d0.638
f_chiral_restr0.039
f_bond_d0.003
f_plane_restr0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2924
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms29

Software

Software
Software NamePurpose
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection