3DX8

Crystal Structure of B*4405 presenting a 10mer EBV epitope


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6293Citrate, Ammonium Acetate, PEG 4000, pH 5.6, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5651.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.776α = 90
b = 82.351β = 90
c = 110.138γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-04-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.165.942669126691

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.165.942669126568134495.940.1970.1970.1930.255RANDOM29.388
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]
-0.78-1.191.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.698
r_dihedral_angle_4_deg17.084
r_dihedral_angle_3_deg14.761
r_dihedral_angle_1_deg9.507
r_scangle_it4.959
r_scbond_it3.894
r_mcangle_it2.624
r_mcbond_it2.139
r_angle_refined_deg1.435
r_angle_other_deg0.907
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.698
r_dihedral_angle_4_deg17.084
r_dihedral_angle_3_deg14.761
r_dihedral_angle_1_deg9.507
r_scangle_it4.959
r_scbond_it3.894
r_mcangle_it2.624
r_mcbond_it2.139
r_angle_refined_deg1.435
r_angle_other_deg0.907
r_mcbond_other0.38
r_symmetry_vdw_other0.224
r_nbd_other0.196
r_nbd_refined0.188
r_nbtor_refined0.176
r_symmetry_hbond_refined0.171
r_xyhbond_nbd_refined0.135
r_chiral_restr0.102
r_symmetry_vdw_refined0.089
r_nbtor_other0.082
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3178
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms12

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling