4P27

Structure of Schistosoma mansoni venom allergen-like protein 4 (SmVAL4)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.085 M sodium acetate trihydrate at pH 4.6, 25% (w/v) PEG 2000, 0.17 M ammonium sulfate and 15% (v/v) glycerol, 8 mg/ml SmVAL4 in Sodium Citrate at pH 5.0
Crystal Properties
Matthews coefficientSolvent content
3.9668.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.645α = 90
b = 78.645β = 90
c = 83.52γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTC2013-12-19SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.1534.0599.70.0715.121.215770
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.2399.30.760.693121.2

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 DIFFRACTIONTHROUGHOUT2.1628.631494780399.760.181880.180390.20877RANDOM39.084
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]
0.030.03-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined9.583
r_scbond_it6.558
r_mcangle_it5.49
r_mcbond_it4.107
r_angle_refined_deg2.253
r_chiral_restr0.159
r_bond_refined_d0.023
r_gen_planes_refined0.014
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined9.583
r_scbond_it6.558
r_mcangle_it5.49
r_mcbond_it4.107
r_angle_refined_deg2.253
r_chiral_restr0.159
r_bond_refined_d0.023
r_gen_planes_refined0.014
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
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_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
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 Atoms1258
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement