4FXA

Crystal structure of the complex of Ribosome inactivating protein from Momordica balsamina with N-acetyl arginine at 1.7 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4F9N 

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
2.4249.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.357α = 90
b = 130.357β = 90
c = 40.022γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHMirror2012-05-22MSINGLE 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
11.765.299.20.096727779
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)
11.71.7694.70.35962.1

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 REPLACEMENTTHROUGHOUT4F9N1.765.1825027139599.70.188620.18620.23594RANDOM31.999
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]
-1.03-0.51-1.031.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.066
r_dihedral_angle_4_deg21.636
r_dihedral_angle_3_deg12.438
r_scangle_it5.947
r_dihedral_angle_1_deg5.532
r_scbond_it3.817
r_mcangle_it2.334
r_angle_refined_deg2.123
r_mcbond_it1.497
r_chiral_restr0.161
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.066
r_dihedral_angle_4_deg21.636
r_dihedral_angle_3_deg12.438
r_scangle_it5.947
r_dihedral_angle_1_deg5.532
r_scbond_it3.817
r_mcangle_it2.334
r_angle_refined_deg2.123
r_mcbond_it1.497
r_chiral_restr0.161
r_bond_refined_d0.028
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1910
Nucleic Acid Atoms
Solvent Atoms227
Heterogen Atoms41

Software

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