4Z8S

Structural studies on a non-toxic homologue of type II RIPs from Momordica charantia (bitter gourd)-Native-1


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.32980.1M HEPES, 20% w/v PEG 10000
Crystal Properties
Matthews coefficientSolvent content
3.6266.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.97α = 90
b = 134.21β = 90
c = 44.67γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2009-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54179

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
12.3629.471000.1112.263683927
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.362.491003.186

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 REPLACEMENTTHROUGHOUT1HWM2.3629.4734922186199.90.166520.164650.20144RANDOM28.97
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]
2.47-1.82-0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.982
r_dihedral_angle_4_deg16.376
r_dihedral_angle_3_deg13.522
r_dihedral_angle_1_deg6.671
r_long_range_B_refined6.009
r_long_range_B_other6.009
r_scangle_other4.085
r_mcangle_it2.878
r_mcangle_other2.877
r_scbond_it2.548
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.982
r_dihedral_angle_4_deg16.376
r_dihedral_angle_3_deg13.522
r_dihedral_angle_1_deg6.671
r_long_range_B_refined6.009
r_long_range_B_other6.009
r_scangle_other4.085
r_mcangle_it2.878
r_mcangle_other2.877
r_scbond_it2.548
r_scbond_other2.548
r_mcbond_it1.808
r_mcbond_other1.807
r_angle_refined_deg1.617
r_angle_other_deg1.175
r_chiral_restr0.133
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 Atoms3944
Nucleic Acid Atoms
Solvent Atoms407
Heterogen Atoms112

Software

Software
Software NamePurpose
REFMACrefinement