3N3X

Crystal Structure of the complex formed between type I ribosome inactivating protein and hexapeptide Ser-Asp-Asp-Asp-Met-Gly at 1.7 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AHA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.729814% PEG6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3547.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.241α = 90
b = 130.241β = 90
c = 39.974γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHmirror2009-07-20MSINGLE 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
11.74099.20.03856.9277452774525.2
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)
11.71.7692.80.284.9

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 REPLACEMENTTHROUGHOUT1AHA1.737.62774526128138499.170.21050.209960.197720.22165RANDOM28.068
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]
-1.06-0.53-1.061.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.747
r_dihedral_angle_4_deg16.474
r_dihedral_angle_3_deg14.298
r_dihedral_angle_1_deg5.184
r_scangle_it2.65
r_scbond_it1.669
r_angle_refined_deg1.195
r_mcangle_it1.024
r_mcbond_it0.583
r_symmetry_hbond_refined0.526
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.747
r_dihedral_angle_4_deg16.474
r_dihedral_angle_3_deg14.298
r_dihedral_angle_1_deg5.184
r_scangle_it2.65
r_scbond_it1.669
r_angle_refined_deg1.195
r_mcangle_it1.024
r_mcbond_it0.583
r_symmetry_hbond_refined0.526
r_nbtor_refined0.305
r_symmetry_vdw_refined0.272
r_nbd_refined0.207
r_xyhbond_nbd_refined0.113
r_chiral_restr0.078
r_bond_refined_d0.008
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1954
Nucleic Acid Atoms
Solvent Atoms258
Heterogen Atoms39

Software

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