1W8K

Crystal structure of apical membrane antigen 1 from Plasmodium vivax


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17THE CRYSTALLISATION MIXTURE CONSISTED OF 10-12% (W/V) PEG3350, 100-200MM IMIDAZOLE, PH 7.0, 5-10% (V/V) ISOPROPANOL, AND 1% (V/V) DMF OR 3% (V/V) T-BUTANOL. THE PROTEIN SOLUTION WAS DILUTED BY 40 - 60% REMARK 280 WITH THE CRYSTALLISATION BUFFER, GIVING A FINAL REMARK 280 CONCENTRATION OF 4-6 MG. ML-1 IN SUSPENDED DROPS OF VOLUME REMARK 280 2 - 3 PERCENT.
Crystal Properties
Matthews coefficientSolvent content
2.244

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.03α = 90
b = 53.76β = 113.18
c = 60.29γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2004-02-14MSINGLE 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
11.83099.20.0610.53.7152093
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)
11.81.997.30.742

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 DIFFRACTIONMADTHROUGHOUT1.819.3438819207099.70.2220.2190.269RANDOM41.09
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]
0.651.73-1.972.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.4
r_dihedral_angle_4_deg19.969
r_dihedral_angle_3_deg17.131
r_dihedral_angle_1_deg7.154
r_scangle_it5.586
r_scbond_it3.935
r_mcangle_it3.473
r_mcbond_it2.384
r_angle_refined_deg1.926
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.4
r_dihedral_angle_4_deg19.969
r_dihedral_angle_3_deg17.131
r_dihedral_angle_1_deg7.154
r_scangle_it5.586
r_scbond_it3.935
r_mcangle_it3.473
r_mcbond_it2.384
r_angle_refined_deg1.926
r_nbtor_refined0.317
r_symmetry_hbond_refined0.24
r_xyhbond_nbd_refined0.228
r_nbd_refined0.221
r_symmetry_vdw_refined0.169
r_chiral_restr0.13
r_bond_refined_d0.02
r_gen_planes_refined0.009
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 Atoms2932
Nucleic Acid Atoms
Solvent Atoms213
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing