3SJ6

Crystal Structure of the complex of type I ribosome inactivating protein from momordica balsamina with 5-(hydroxymethyl)oxalane-2,3,4-triol at 1.6 A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

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
2.4149.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.972α = 90
b = 129.972β = 90
c = 40.245γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHmirror2009-07-24MSINGLE 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
11.665990.0851.5313793137920.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6392.80.314.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1AHA1.664.993137931379167799.060.171090.171080.169780.19542RANDOM23.459
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]
-0.74-0.37-0.741.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.21
r_dihedral_angle_4_deg19.254
r_dihedral_angle_3_deg12.22
r_dihedral_angle_1_deg5.196
r_scangle_it3.923
r_scbond_it2.407
r_mcangle_it1.406
r_angle_refined_deg1.339
r_mcbond_it0.739
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.21
r_dihedral_angle_4_deg19.254
r_dihedral_angle_3_deg12.22
r_dihedral_angle_1_deg5.196
r_scangle_it3.923
r_scbond_it2.407
r_mcangle_it1.406
r_angle_refined_deg1.339
r_mcbond_it0.739
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1911
Nucleic Acid Atoms
Solvent Atoms312
Heterogen Atoms36

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling