5DSS

MP-4 contributes to snake venom neutralization by Mucuna pruriens seeds through stimulation of cross-reactive antibodies


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R8N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.529850 mM Tris-HCl pH 9.5, 1.5 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
1.935.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51α = 90
b = 69.18β = 90
c = 45.32γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateosmic focusing mirrors2009-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
12.837.9195.50.07325.69.74048
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.959414.510.1

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 REPLACEMENTTHROUGHOUT1R8N2.837.91385118594.720.267620.266790.28439RANDOM22.988
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]
-0.193.03-2.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.049
r_dihedral_angle_3_deg27.896
r_dihedral_angle_4_deg18.882
r_dihedral_angle_1_deg13.576
r_angle_refined_deg1.645
r_chiral_restr0.148
r_gen_planes_refined0.022
r_bond_refined_d0.012
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.049
r_dihedral_angle_3_deg27.896
r_dihedral_angle_4_deg18.882
r_dihedral_angle_1_deg13.576
r_angle_refined_deg1.645
r_chiral_restr0.148
r_gen_planes_refined0.022
r_bond_refined_d0.012
r_bond_other_d
r_angle_other_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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms1411
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata processing
SCALAdata scaling
Cootmodel building
MAR345dtbdata collection