4IRV

Structure of the Helicobacter pylori CagA Oncogene Bound to the Human Tumor Suppressor Apoptosis-stimulating Protein of p53-2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5Crystals were grown by vapor diffusion at 25 degrees C using hanging drops formed from mixing a 2ul of the protein complex with 2ul of an equilibration buffer (21% polyethylene glycol (PEG) molecular weight 4 kDa, 200 mM Li2 SO4 , and 100 mM Tris pH 8.5) and 0.6ul of the Silver Bullets additive 43 (Hampton Research HR2-996-43). Significantly higher quality crystals were obtained from selenomethionine-substituted protein complexes and they were used for the final refinement, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.5351.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.641α = 90
b = 120.239β = 115.64
c = 100.659γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.97869NSLSX29A

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
12.0490.7580050

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.0490.7573785391596.710.191480.189270.2341RANDOM34
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]
-2.060.24-0.992
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.834
r_dihedral_angle_4_deg24.42
r_dihedral_angle_3_deg16.826
r_dihedral_angle_1_deg5.511
r_angle_refined_deg1.909
r_angle_other_deg0.904
r_chiral_restr0.117
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.834
r_dihedral_angle_4_deg24.42
r_dihedral_angle_3_deg16.826
r_dihedral_angle_1_deg5.511
r_angle_refined_deg1.909
r_angle_other_deg0.904
r_chiral_restr0.117
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7017
Nucleic Acid Atoms
Solvent Atoms513
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement