5ILX

Crystal structure of Ribosome inactivating protein from Momordica balsamina with Uracil at 1.70 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4FPZ 

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
2.3748

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
11.765.091000.0437.2227751
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.7299.90.442.7

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 REPLACEMENTTHROUGHOUT4FPZ1.765.0926350139599.990.163460.161060.21017RANDOM25.713
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]
-0.69-0.35-0.692.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.589
r_dihedral_angle_4_deg21.393
r_dihedral_angle_3_deg12.59
r_long_range_B_other6.797
r_long_range_B_refined6.795
r_dihedral_angle_1_deg5.866
r_scangle_other5.069
r_scbond_it3.469
r_scbond_other3.436
r_mcangle_it3.119
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.589
r_dihedral_angle_4_deg21.393
r_dihedral_angle_3_deg12.59
r_long_range_B_other6.797
r_long_range_B_refined6.795
r_dihedral_angle_1_deg5.866
r_scangle_other5.069
r_scbond_it3.469
r_scbond_other3.436
r_mcangle_it3.119
r_mcangle_other3.118
r_mcbond_it2.409
r_mcbond_other2.4
r_angle_refined_deg2.013
r_angle_other_deg1.101
r_chiral_restr0.116
r_bond_refined_d0.021
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 Atoms1910
Nucleic Acid Atoms
Solvent Atoms258
Heterogen Atoms26

Software

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