3N2D

Crystal Structure of the Complex of type I Ribosome inactivating protein with hexapeptide Ser-Asp-Asp-Asp-Met-Gly at 2.2 A resolution


X-RAY DIFFRACTION

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
2.4349.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.186α = 90
b = 131.186β = 90
c = 40.734γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMARRESEARCHMirror2009-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5414

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
12.2265.799.20.05612.6129681296842.124
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)
2.222.2996.20.3152

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 1AHA2.2219.84129681226462799.440.186260.186080.182920.2219RANDOM42.229
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]
-1.41-0.7-1.412.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.233
r_dihedral_angle_4_deg25.32
r_dihedral_angle_3_deg17.209
r_dihedral_angle_1_deg5.367
r_scangle_it3.37
r_scbond_it2.148
r_angle_refined_deg1.534
r_mcangle_it1.351
r_mcbond_it0.822
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.233
r_dihedral_angle_4_deg25.32
r_dihedral_angle_3_deg17.209
r_dihedral_angle_1_deg5.367
r_scangle_it3.37
r_scbond_it2.148
r_angle_refined_deg1.534
r_mcangle_it1.351
r_mcbond_it0.822
r_nbtor_refined0.309
r_symmetry_hbond_refined0.26
r_nbd_refined0.217
r_symmetry_vdw_refined0.208
r_xyhbond_nbd_refined0.19
r_chiral_restr0.111
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms1954
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms28

Software

Software
Software NamePurpose
DENZOdata reduction
AMoREphasing
REFMACrefinement
AUTOMARdata reduction
SCALEPACKdata scaling