7NZE

Crystal structure of HLA-DR4 in complex with a human collagen type II peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6BIL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION29020% polyethylene glycol 3350 and 200 mM ammonium chloride
Crystal Properties
Matthews coefficientSolvent content
2.8656.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.418α = 90
b = 71.84β = 111.331
c = 125.721γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.0547.00998.10.9998.2162583
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.10.8511

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-VALUE6BIL2.0547.00962583306197.8820.1940.1920.244946.285
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]
-0.63-0.3780.5920.255
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.774
r_dihedral_angle_4_deg20.232
r_dihedral_angle_3_deg16.161
r_dihedral_angle_1_deg8.377
r_lrange_it5.653
r_lrange_other5.58
r_scangle_it3.063
r_scangle_other3.062
r_mcangle_it2.396
r_mcangle_other2.396
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.774
r_dihedral_angle_4_deg20.232
r_dihedral_angle_3_deg16.161
r_dihedral_angle_1_deg8.377
r_lrange_it5.653
r_lrange_other5.58
r_scangle_it3.063
r_scangle_other3.062
r_mcangle_it2.396
r_mcangle_other2.396
r_scbond_it1.911
r_scbond_other1.911
r_angle_refined_deg1.844
r_mcbond_it1.528
r_mcbond_other1.528
r_angle_other_deg1.318
r_symmetry_nbd_refined0.415
r_nbd_other0.268
r_nbd_refined0.21
r_xyhbond_nbd_refined0.191
r_symmetry_nbd_other0.19
r_nbtor_refined0.173
r_symmetry_xyhbond_nbd_refined0.152
r_chiral_restr0.082
r_symmetry_nbtor_other0.081
r_symmetry_xyhbond_nbd_other0.076
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6330
Nucleic Acid Atoms
Solvent Atoms346
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACdata reduction
REFMACrefinement
xia2data reduction
Aimlessdata scaling