3N31

Crystal Structure of the complex of type I ribosome inactivating protein with fucose at 2.1A 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
2.3347.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.153α = 90
b = 129.153β = 90
c = 39.366γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMAR CCD 165 mmmirror2008-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8148EMBL/DESY, HAMBURGX13

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
12.164.5897.30.0514.2141921419235.2
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)
12.12.2292.40.1754.7

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 REPLACEMENTTHROUGHOUT1AHA2.1164.58141921313470397.530.178470.176380.173950.22627RANDOM33.838
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]
-2.5-1.25-2.53.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.701
r_dihedral_angle_4_deg20.085
r_dihedral_angle_3_deg15.696
r_dihedral_angle_1_deg6.255
r_scangle_it5.693
r_scbond_it3.712
r_angle_refined_deg2.228
r_mcangle_it2.132
r_mcbond_it1.247
r_chiral_restr0.136
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.701
r_dihedral_angle_4_deg20.085
r_dihedral_angle_3_deg15.696
r_dihedral_angle_1_deg6.255
r_scangle_it5.693
r_scbond_it3.712
r_angle_refined_deg2.228
r_mcangle_it2.132
r_mcbond_it1.247
r_chiral_restr0.136
r_bond_refined_d0.026
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1911
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms45

Software

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