6O9C

Crystal structure of HLA-A3*01 in complex with a mutant beta-catenin peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6O9BPDB entry 6O9B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52920.1 M MES, pH 6.5, 0.2 M ammonium sulfate, 30% PEG5000 MME
Crystal Properties
Matthews coefficientSolvent content
3.0159.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 155.123α = 90
b = 155.123β = 90
c = 85.316γ = 120
Symmetry
Space GroupP 6 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2018-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-10.918394NSLS-II17-ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
12.4544.7899.90.1720.1770.99813.8918.0892262048.941
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.452.5299.71.3961.4340.7672.1418.839

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 REPLACEMENTTHROUGHOUTPDB entry 6O9B2.4544.7821494113299.820.2160.21370.259RANDOM47.758
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]
0.540.270.54-1.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.266
r_dihedral_angle_4_deg22.328
r_dihedral_angle_3_deg17.261
r_dihedral_angle_1_deg7.472
r_angle_refined_deg1.619
r_angle_other_deg1.481
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.266
r_dihedral_angle_4_deg22.328
r_dihedral_angle_3_deg17.261
r_dihedral_angle_1_deg7.472
r_angle_refined_deg1.619
r_angle_other_deg1.481
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3161
Nucleic Acid Atoms
Solvent Atoms43
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction