2J4W

Structure of a Plasmodium vivax apical membrane antigen 1-Fab F8.12.19 complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.4PVAMA1 AND FAB-F8.12.19 WERE MIXED IN A 1:1 STOICHIOMETRIC RATIO AND LEFT TO INCUBATE FOR 4 HOURS AT ROOM TEMPERATURE TO FORM THE ANTIBODY-ANTIGEN COMPLEX BEFORE MIXING WITH CRYSTALLISATION SCREENING BUFFERS. CRYSTALS USED FOR DIFFRACTION MEASUREMENTS WERE OBTAINED AS FOLLOWS. THE CRYSTALLISATION BUFFER IN THE RESERVOIR COMPRISED 10% PEG 6000 AND 0.1 M SODIUM ACETATE BUFFERED TO PH 4.4. THE CRYSTALLISATION DROP WAS PREPARED BY ADDING 0.8 MICROLITRES OF THE CRYSTALLISATION BUFFER TO 0.8 MICROLITRES OF THE PVAMA1-FAB COMPLEX, GIVING A FINAL PROTEIN CONCENTRATION OF 3.9 MG/ML.
Crystal Properties
Matthews coefficientSolvent content
3.6165.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 171.787α = 90
b = 171.787β = 90
c = 44.748γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12.52098.10.1414.81026533-3
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)
12.52.6880.93

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 ENTRIES 2IGF, 1W8K2.52024858133598.70.190.1870.241RANDOM42.31
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]
-2.57-1.28-2.573.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.558
r_dihedral_angle_4_deg23.852
r_dihedral_angle_3_deg20.325
r_dihedral_angle_1_deg7.416
r_scangle_it3.508
r_mcangle_it2.622
r_scbond_it2.547
r_angle_refined_deg1.893
r_mcbond_it1.504
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.558
r_dihedral_angle_4_deg23.852
r_dihedral_angle_3_deg20.325
r_dihedral_angle_1_deg7.416
r_scangle_it3.508
r_mcangle_it2.622
r_scbond_it2.547
r_angle_refined_deg1.893
r_mcbond_it1.504
r_nbtor_refined0.315
r_symmetry_hbond_refined0.233
r_nbd_refined0.228
r_symmetry_vdw_refined0.188
r_xyhbond_nbd_refined0.157
r_chiral_restr0.125
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3606
Nucleic Acid Atoms
Solvent Atoms155
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing