5J5E

crystal structure of antigen-ERAP1 domain complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5277100 mM Tris, pH 8.5 and 16% PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.7555.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.26α = 90
b = 66.85β = 110.16
c = 66.5γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102014-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.1NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.862.43776.62.410114
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)
12.82.9581.30.3352.32.3

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 REPLACEMENTTHROUGHOUT3RJO2.862.43940050075.140.209870.20670.2689RANDOM28.119
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]
0.220.12-0.480.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.657
r_dihedral_angle_4_deg19.68
r_dihedral_angle_3_deg17.236
r_dihedral_angle_1_deg7.009
r_long_range_B_refined4.26
r_long_range_B_other4.259
r_mcangle_it2.773
r_mcangle_other2.772
r_scangle_other2.697
r_mcbond_it1.623
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.657
r_dihedral_angle_4_deg19.68
r_dihedral_angle_3_deg17.236
r_dihedral_angle_1_deg7.009
r_long_range_B_refined4.26
r_long_range_B_other4.259
r_mcangle_it2.773
r_mcangle_other2.772
r_scangle_other2.697
r_mcbond_it1.623
r_mcbond_other1.622
r_angle_refined_deg1.61
r_scbond_it1.573
r_scbond_other1.569
r_angle_other_deg1.022
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
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_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3328
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
xia2data reduction
PHASERphasing