7NZF

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION2900.1 M MIB buffer pH 4.0, 25 % (w/v) PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.3748.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.441α = 90
b = 71.441β = 90
c = 138.049γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.91842DiamondI03

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
11.946.07990.0870.0950.0390.99917.511.132456
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)
11.91.940.8340.9130.370.85311.5

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-VALUE1J8H1.936.95132382156498.440.2240.22140.266735.725
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]
0.140.070.14-0.456
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.878
r_dihedral_angle_3_deg15.723
r_dihedral_angle_4_deg15.493
r_dihedral_angle_1_deg8.225
r_lrange_it4.558
r_lrange_other4.503
r_scangle_it1.843
r_scangle_other1.843
r_angle_refined_deg1.631
r_mcangle_it1.525
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.878
r_dihedral_angle_3_deg15.723
r_dihedral_angle_4_deg15.493
r_dihedral_angle_1_deg8.225
r_lrange_it4.558
r_lrange_other4.503
r_scangle_it1.843
r_scangle_other1.843
r_angle_refined_deg1.631
r_mcangle_it1.525
r_mcangle_other1.525
r_angle_other_deg1.293
r_scbond_it1.158
r_scbond_other1.157
r_mcbond_it0.948
r_mcbond_other0.947
r_nbd_refined0.22
r_symmetry_nbd_refined0.205
r_symmetry_nbd_other0.189
r_nbd_other0.183
r_xyhbond_nbd_refined0.175
r_nbtor_refined0.17
r_symmetry_xyhbond_nbd_refined0.158
r_symmetry_nbtor_other0.081
r_chiral_restr0.078
r_xyhbond_nbd_other0.045
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3022
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
XDSdata scaling