4JTB

Crystal structure of Ribosome inactivating protein from Momordica balsamina complexed with phosphate ion at 1.71 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
2.4249.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.153α = 90
b = 133.153β = 90
c = 38.397γ = 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
11.7166.61000.06913.12743027430
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)
11.711.771000.472

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 REPLACEMENTTHROUGHOUT4G2X1.7166.5826055137799.970.214380.212210.25646RANDOM29.078
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]
-0.75-0.75-0.752.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.031
r_dihedral_angle_3_deg16.054
r_dihedral_angle_4_deg14.085
r_dihedral_angle_1_deg5.92
r_angle_other_deg3.811
r_scbond_it3.037
r_angle_refined_deg2.143
r_mcangle_it2.128
r_mcbond_it1.495
r_mcbond_other1.495
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.031
r_dihedral_angle_3_deg16.054
r_dihedral_angle_4_deg14.085
r_dihedral_angle_1_deg5.92
r_angle_other_deg3.811
r_scbond_it3.037
r_angle_refined_deg2.143
r_mcangle_it2.128
r_mcbond_it1.495
r_mcbond_other1.495
r_chiral_restr0.161
r_bond_refined_d0.028
r_gen_planes_other0.015
r_gen_planes_refined0.01
r_bond_other_d
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 Atoms157
Heterogen Atoms19

Software

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