4JTP

Crystal structure of Ribosome inactivating protein from Momordica balsamina complexed with Ascorbic acid at 1.85 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
2.2545.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.38α = 90
b = 130.38β = 90
c = 37.226γ = 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
11.8537.671000.05244.32015120151
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.881003

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 REPLACEMENTTHROUGHOUT4G2X1.8537.619118102799.770.169340.16670.22362RANDOM32.421
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]
-0.84-0.84-0.842.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.3
r_dihedral_angle_4_deg19.879
r_dihedral_angle_3_deg13.892
r_dihedral_angle_1_deg5.717
r_angle_other_deg3.656
r_angle_refined_deg1.979
r_chiral_restr0.121
r_bond_refined_d0.019
r_gen_planes_other0.019
r_gen_planes_refined0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.3
r_dihedral_angle_4_deg19.879
r_dihedral_angle_3_deg13.892
r_dihedral_angle_1_deg5.717
r_angle_other_deg3.656
r_angle_refined_deg1.979
r_chiral_restr0.121
r_bond_refined_d0.019
r_gen_planes_other0.019
r_gen_planes_refined0.009
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1910
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms26

Software

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