3MRB

Crystal Structure of MHC class I HLA-A2 molecule complexed with HCMV pp65-495-503 nonapeptide A7H variant


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529312% PEG 6000, 0.1M NaCacodylate, 5mg/ml protein conc., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5251.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.36α = 90
b = 81.09β = 112.93
c = 56.79γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-07-03MSINGLE 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
11.45096.50.06613.074.2184555-321.14
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)
11.41.4595.10.323.2

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 3GSO1.41582657820194.540.2140.2120.244RANDOM18.341
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]
-0.32-1.04-0.590.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.264
r_dihedral_angle_4_deg15.364
r_dihedral_angle_3_deg13.203
r_dihedral_angle_1_deg5.912
r_scangle_it2.433
r_mcangle_it1.795
r_scbond_it1.786
r_angle_refined_deg1.295
r_mcbond_it1.115
r_chiral_restr0.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.264
r_dihedral_angle_4_deg15.364
r_dihedral_angle_3_deg13.203
r_dihedral_angle_1_deg5.912
r_scangle_it2.433
r_mcangle_it1.795
r_scbond_it1.786
r_angle_refined_deg1.295
r_mcbond_it1.115
r_chiral_restr0.089
r_bond_refined_d0.01
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3155
Nucleic Acid Atoms
Solvent Atoms387
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
AMoREphasing