4L29

Structure of wtMHC class I with NY-ESO1 double mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2931.9 M ammonium sulphate, 2% PEG 6K, 100 mM Tris-HCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.9769.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.57α = 90
b = 313.36β = 90
c = 314.46γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARMOSAIC 225 mm CCDbent collimating mirror and toroid2013-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM141.0716ESRFBM14

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
13.0953.881000.1929.35.8182537182537
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)
13.093.271000.010152.25.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3.0953.8173264915598.820.172080.170580.20054RANDOM48.226
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]
-295.7123.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.327
r_dihedral_angle_4_deg16.144
r_dihedral_angle_3_deg15.895
r_dihedral_angle_1_deg6.095
r_scangle_it1.668
r_angle_refined_deg1.159
r_scbond_it0.952
r_mcangle_it0.91
r_angle_other_deg0.772
r_mcbond_it0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.327
r_dihedral_angle_4_deg16.144
r_dihedral_angle_3_deg15.895
r_dihedral_angle_1_deg6.095
r_scangle_it1.668
r_angle_refined_deg1.159
r_scbond_it0.952
r_mcangle_it0.91
r_angle_other_deg0.772
r_mcbond_it0.48
r_chiral_restr0.068
r_mcbond_other0.057
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_mcangle_other
r_nbtor_other
r_scbond_other
r_xyhbond_nbd_refined
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms44422
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms150

Software

Software
Software NamePurpose
MxCuBEdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing