6QZD

HLA-DR1 with SGP Influenza Matrix Peptide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52910.1 M Tris 0.2 M NH4 SO4 25% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.5852.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.42α = 90
b = 76.73β = 93.5
c = 90.13γ = 90
Symmetry
Space GroupP 1 21 1

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)Rrim I (All)Rpim I (All)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
12.6655.5499.10.1960.2290.1166.33.726304
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)
12.662.7398.71.0431.2150.6160.4661.5

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-VALUE1DLH2.6655.53726290126798.950.2030.20010.253942.325
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]
-2.4410.044-0.0722.489
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.351
r_dihedral_angle_4_deg21.793
r_dihedral_angle_3_deg20.234
r_dihedral_angle_1_deg7.858
r_lrange_it4.913
r_scangle_it2.228
r_mcangle_it1.989
r_angle_refined_deg1.684
r_scbond_it1.373
r_mcbond_it1.134
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.351
r_dihedral_angle_4_deg21.793
r_dihedral_angle_3_deg20.234
r_dihedral_angle_1_deg7.858
r_lrange_it4.913
r_scangle_it2.228
r_mcangle_it1.989
r_angle_refined_deg1.684
r_scbond_it1.373
r_mcbond_it1.134
r_nbtor_refined0.317
r_symmetry_nbd_refined0.245
r_nbd_refined0.231
r_xyhbond_nbd_refined0.176
r_ncsr_local_group_30.164
r_symmetry_xyhbond_nbd_refined0.142
r_chiral_restr0.127
r_ncsr_local_group_10.098
r_ncsr_local_group_20.092
r_bond_refined_d0.01
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6262
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
XDSdata scaling
Aimlessdata scaling
PHASERphasing