4KL4

Crystal structure of Ribosome inactivating protein from Momordica balsamina complexed with Polyethylene glycol at 1.90 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4G2X 

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
2.3347.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.411α = 90
b = 130.411β = 90
c = 38.627γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHMirror2012-11-17MSINGLE 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
11.965.211000.06650.51929819298
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.931002.6

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 REPLACEMENTTHROUGHOUT4G2X1.965.211830698899.980.182290.179570.23267RANDOM39.739
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]
-2.31-1.15-2.313.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.683
r_dihedral_angle_4_deg20.708
r_dihedral_angle_3_deg14.869
r_dihedral_angle_1_deg5.407
r_scangle_it5.351
r_scbond_it3.419
r_mcangle_it1.985
r_angle_refined_deg1.805
r_mcbond_it1.174
r_chiral_restr0.139
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.683
r_dihedral_angle_4_deg20.708
r_dihedral_angle_3_deg14.869
r_dihedral_angle_1_deg5.407
r_scangle_it5.351
r_scbond_it3.419
r_mcangle_it1.985
r_angle_refined_deg1.805
r_mcbond_it1.174
r_chiral_restr0.139
r_bond_refined_d0.024
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1910
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms27

Software

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