3CPL

Crystal Structure of H-2Db in complex with a variant M6A of the NP366 peptide from influenza A virus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YN7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1M potassium thiocianate, 30% PEG 2000, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6854.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.71α = 99.95
b = 69.7β = 111.04
c = 72.38γ = 110.48
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2008-01-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE1.514

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
12.550950.09413.692.6321623054920.343
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.52.693.90.27352.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1YN72.51530430306995.380.2270.220.286RANDOM14.635
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]
-0.360.250.290.26-0.490.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.26
r_dihedral_angle_3_deg21.113
r_dihedral_angle_4_deg20.588
r_dihedral_angle_1_deg6.916
r_scangle_it1.663
r_mcangle_it1.601
r_angle_refined_deg1.422
r_scbond_it1.114
r_mcbond_it0.915
r_symmetry_hbond_refined0.402
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.26
r_dihedral_angle_3_deg21.113
r_dihedral_angle_4_deg20.588
r_dihedral_angle_1_deg6.916
r_scangle_it1.663
r_mcangle_it1.601
r_angle_refined_deg1.422
r_scbond_it1.114
r_mcbond_it0.915
r_symmetry_hbond_refined0.402
r_symmetry_vdw_refined0.342
r_nbtor_refined0.33
r_nbd_refined0.274
r_xyhbond_nbd_refined0.24
r_chiral_restr0.094
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6385
Nucleic Acid Atoms
Solvent Atoms32
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
XDSdata reduction