3MRD

Crystal Structure of MHC class I HLA-A2 molecule complexed with HCMV pp65-495-503 nonapeptide V6G 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 DROP6.529310% PEG 6000, 0.1M MES, 5mg/ml protein conc., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.550.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.14α = 90
b = 80.92β = 112.41
c = 56.2γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2006-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97949ESRFID29

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
11.72097.40.08912.423.9947219-321.826
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)
11.71.898.70.3725.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3GSO1.714.9346627468196.560.1960.1940.226RANDOM20.763
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.141
r_dihedral_angle_4_deg17.005
r_dihedral_angle_3_deg13.194
r_dihedral_angle_1_deg5.677
r_scangle_it4.513
r_mcangle_it3.76
r_scbond_it3.169
r_mcbond_it2.694
r_angle_refined_deg1.389
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.141
r_dihedral_angle_4_deg17.005
r_dihedral_angle_3_deg13.194
r_dihedral_angle_1_deg5.677
r_scangle_it4.513
r_mcangle_it3.76
r_scbond_it3.169
r_mcbond_it2.694
r_angle_refined_deg1.389
r_nbtor_refined0.305
r_nbd_refined0.209
r_symmetry_hbond_refined0.201
r_symmetry_vdw_refined0.195
r_xyhbond_nbd_refined0.16
r_chiral_restr0.1
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3130
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
AMoREphasing