5DOM

Crystal structure, maturation and flocculating properties of a 2S albumin from Moringa oleifera seeds


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.3293Initial: 0.1 M sodium acetate pH 4.6 and 2.0 M NaCl, Optimization: 0.1 M sodium acetate pH 4.3 and 2.4 M NaCl
Crystal Properties
Matthews coefficientSolvent content
2.1643

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.867α = 90
b = 106.867β = 90
c = 43.16γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-03-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.45LNLSW01B-MX2

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
11.74099.616.966.71367413674
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.81

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 DIFFRACTIONSIRASTHROUGHOUT1.6975.571199260888.570.223910.221920.26288RANDOM35.896
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]
0.320.32-0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.857
r_dihedral_angle_4_deg20.593
r_dihedral_angle_3_deg15.72
r_long_range_B_refined8.516
r_long_range_B_other8.512
r_scangle_other6.694
r_dihedral_angle_1_deg6.217
r_mcangle_it4.971
r_mcangle_other4.966
r_scbond_it4.397
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.857
r_dihedral_angle_4_deg20.593
r_dihedral_angle_3_deg15.72
r_long_range_B_refined8.516
r_long_range_B_other8.512
r_scangle_other6.694
r_dihedral_angle_1_deg6.217
r_mcangle_it4.971
r_mcangle_other4.966
r_scbond_it4.397
r_scbond_other4.392
r_mcbond_it3.637
r_mcbond_other3.582
r_angle_refined_deg2.018
r_angle_other_deg1.141
r_chiral_restr0.156
r_bond_refined_d0.022
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms740
Nucleic Acid Atoms
Solvent Atoms50
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
HKL-2000data collection