5Y48

Crystal structure of the complex of Ribosome inactivating protein from Momordica balsamina with Pyrimidine-2,4-dione at 1.70 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5ILX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.729814% PEG 6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4148.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.186α = 90
b = 130.186β = 90
c = 39.976γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDMARRESEARCH2012-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

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
11.765.091000.0411.3227751
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.7011.74599.92.7

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 REPLACEMENTTHROUGHOUT5ILX1.765.0926352139599.990.166270.164010.21029RANDOM25.218
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]
-0.7-0.35-0.72.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.845
r_dihedral_angle_4_deg19.895
r_dihedral_angle_3_deg12.553
r_long_range_B_refined6.374
r_long_range_B_other6.214
r_dihedral_angle_1_deg5.809
r_scangle_other5.014
r_scbond_it3.44
r_scbond_other3.439
r_mcangle_it3.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.845
r_dihedral_angle_4_deg19.895
r_dihedral_angle_3_deg12.553
r_long_range_B_refined6.374
r_long_range_B_other6.214
r_dihedral_angle_1_deg5.809
r_scangle_other5.014
r_scbond_it3.44
r_scbond_other3.439
r_mcangle_it3.079
r_mcangle_other3.078
r_mcbond_it2.385
r_mcbond_other2.377
r_angle_refined_deg2.007
r_angle_other_deg1.098
r_chiral_restr0.121
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.003
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 Atoms1910
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing