3MRG

Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081 nonapeptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GSOPDB ENTRY 3GSO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529317% PEG 6000, 0.1M NaCitrate, 0.05M NaCl, 5mg/ml protein conc., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3848.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.12α = 90
b = 80.87β = 112.33
c = 56.2γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.93300ESRFID14-2

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
11.32097.20.12510.154.53104890-318.12
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)
11.31.487.30.3132.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3GSO1.3151017981027294.560.180.1790.202RANDOM15.863
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]
-0.14-0.36-0.230.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.026
r_dihedral_angle_4_deg15.836
r_dihedral_angle_3_deg12.93
r_dihedral_angle_1_deg5.593
r_scangle_it2.531
r_scbond_it1.718
r_mcangle_it1.716
r_angle_refined_deg1.231
r_mcbond_it0.997
r_chiral_restr0.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.026
r_dihedral_angle_4_deg15.836
r_dihedral_angle_3_deg12.93
r_dihedral_angle_1_deg5.593
r_scangle_it2.531
r_scbond_it1.718
r_mcangle_it1.716
r_angle_refined_deg1.231
r_mcbond_it0.997
r_chiral_restr0.092
r_bond_refined_d0.009
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3144
Nucleic Acid Atoms
Solvent Atoms562
Heterogen Atoms13

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
AMoREphasing