3MRL

Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081 nonapeptide C6V variant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MRGPDB ENTRY 3MRG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529315% PEG 6000, 0.1M NaCitrate, 3.6mg/ml protein conc., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4349.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.634α = 90
b = 80.973β = 113.17
c = 57.019γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2006-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.97569ESRFID14-4

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
12.45093.90.1337.822.9916618-340.304
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)
12.42.4890.20.5532.9

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 3MRG2.411515691159990.880.2050.20.279RANDOM31.59
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]
0.33-1.28-1.23-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.645
r_dihedral_angle_4_deg18.935
r_dihedral_angle_3_deg17.882
r_dihedral_angle_1_deg5.99
r_scangle_it2.909
r_mcangle_it1.988
r_scbond_it1.843
r_angle_refined_deg1.223
r_mcbond_it1.064
r_chiral_restr0.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.645
r_dihedral_angle_4_deg18.935
r_dihedral_angle_3_deg17.882
r_dihedral_angle_1_deg5.99
r_scangle_it2.909
r_mcangle_it1.988
r_scbond_it1.843
r_angle_refined_deg1.223
r_mcbond_it1.064
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3145
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
AMoREphasing