7O00

Crystal structure of HLA-DR4 in complex with a HSP70 peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J8H 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION2900.03 M of each divalent cation (12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD), 0.1 M MOPS/HEPES-Na pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.8957.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.23α = 90
b = 76.23β = 90
c = 170.66γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9762DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
12.2456.8999.80.2370.2460.0660.9991225.625047
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.242.313.4743.6050.9610.63526.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1J8H2.2451.45322463110589.6910.2010.19850.242253.581
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]
-0.036-0.0360.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.629
r_dihedral_angle_3_deg19.352
r_dihedral_angle_4_deg17.579
r_dihedral_angle_1_deg8.263
r_lrange_it5.844
r_lrange_other5.826
r_scangle_it4.008
r_scangle_other4.007
r_mcangle_it2.809
r_mcangle_other2.808
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.629
r_dihedral_angle_3_deg19.352
r_dihedral_angle_4_deg17.579
r_dihedral_angle_1_deg8.263
r_lrange_it5.844
r_lrange_other5.826
r_scangle_it4.008
r_scangle_other4.007
r_mcangle_it2.809
r_mcangle_other2.808
r_scbond_it2.486
r_scbond_other2.484
r_mcbond_it1.764
r_mcbond_other1.764
r_angle_refined_deg1.659
r_angle_other_deg1.213
r_symmetry_xyhbond_nbd_refined0.228
r_symmetry_nbd_refined0.201
r_nbd_refined0.199
r_nbd_other0.19
r_symmetry_nbd_other0.186
r_xyhbond_nbd_refined0.184
r_nbtor_refined0.174
r_symmetry_nbtor_other0.081
r_chiral_restr0.07
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3057
Nucleic Acid Atoms
Solvent Atoms80
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
XDSdata reduction
XDSdata scaling