6QZC

HLA-DR1 with the QAR Peptide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION62910.1 M Na Cacodylate, 0.2 M NH4 SO4, 20% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.5251.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.06α = 90
b = 116.08β = 90
c = 43.68γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2016-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97626DiamondI03

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
11.6471.1699.80.09410.37.156957
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.641.681.9120.7530.518

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-VALUE1DLH1.6471.15656904281999.7970.2040.20180.239936.371
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]
-1.414-1.4922.906
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.518
r_dihedral_angle_1_deg23.335
r_dihedral_angle_4_deg17.954
r_dihedral_angle_3_deg14.971
r_dihedral_angle_other_3_deg11.96
r_lrange_it6.927
r_lrange_other6.866
r_scangle_it2.263
r_scangle_other2.257
r_angle_refined_deg1.687
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.518
r_dihedral_angle_1_deg23.335
r_dihedral_angle_4_deg17.954
r_dihedral_angle_3_deg14.971
r_dihedral_angle_other_3_deg11.96
r_lrange_it6.927
r_lrange_other6.866
r_scangle_it2.263
r_scangle_other2.257
r_angle_refined_deg1.687
r_mcangle_it1.685
r_mcangle_other1.685
r_scbond_it1.47
r_scbond_other1.467
r_angle_other_deg1.349
r_mcbond_it1.063
r_mcbond_other1.063
r_symmetry_nbd_refined0.271
r_nbd_other0.212
r_nbd_refined0.205
r_symmetry_xyhbond_nbd_refined0.188
r_symmetry_nbd_other0.186
r_xyhbond_nbd_refined0.174
r_nbtor_refined0.166
r_chiral_restr0.079
r_symmetry_nbtor_other0.079
r_symmetry_xyhbond_nbd_other0.017
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3135
Nucleic Acid Atoms
Solvent Atoms220
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
XDSdata scaling
PHASERphasing