3N1D

Crystal structure of the complex of type I ribosome inactivating protein with ribose at 1.7A 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
2.4249.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.968α = 90
b = 129.968β = 90
c = 40.244γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHmirror2009-07-25MSINGLE 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
11.76599.90.07853263812638123.1
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)
11.799.50.2378

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 REPLACEMENTTHROUGHOUT1AHA1.764.962638126381139899.840.164210.163310.161120.20457RANDOM22.867
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]
-0.78-0.39-0.781.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.353
r_dihedral_angle_4_deg18.118
r_dihedral_angle_3_deg14.013
r_scangle_it6.083
r_dihedral_angle_1_deg5.622
r_scbond_it3.863
r_mcangle_it2.312
r_angle_refined_deg2.233
r_mcbond_it1.372
r_chiral_restr0.176
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.353
r_dihedral_angle_4_deg18.118
r_dihedral_angle_3_deg14.013
r_scangle_it6.083
r_dihedral_angle_1_deg5.622
r_scbond_it3.863
r_mcangle_it2.312
r_angle_refined_deg2.233
r_mcbond_it1.372
r_chiral_restr0.176
r_bond_refined_d0.028
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1906
Nucleic Acid Atoms
Solvent Atoms247
Heterogen Atoms51

Software

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