3MRY

Crystal Structure of type I ribosome inactivating protein from Momordica balsamina with 6-aminopurine at 2.0A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AHAPDB ENTRY 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
2.3848.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.135α = 90
b = 130.135β = 90
c = 39.524γ = 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
1265990.07413.5168501685032.9
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)
122.07930.3164

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1AHA237.57168501570483798.20.184320.183980.180590.2491RANDOM40.413
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]
-2.37-1.19-2.373.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.944
r_dihedral_angle_4_deg21.793
r_dihedral_angle_3_deg15.44
r_dihedral_angle_1_deg6.632
r_scangle_it4.613
r_scbond_it3.234
r_angle_refined_deg2.007
r_mcangle_it1.891
r_mcbond_it1.17
r_chiral_restr0.138
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.944
r_dihedral_angle_4_deg21.793
r_dihedral_angle_3_deg15.44
r_dihedral_angle_1_deg6.632
r_scangle_it4.613
r_scbond_it3.234
r_angle_refined_deg2.007
r_mcangle_it1.891
r_mcbond_it1.17
r_chiral_restr0.138
r_bond_refined_d0.022
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1909
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms44

Software

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