3V14

Crystal structure of the complex of type I Ribosome inactivating protein complexed with Trehalose at 1.70 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MRW 

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
2.4249.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.204α = 90
b = 130.204β = 90
c = 40.148γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHmirror2011-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.75099.90.036332796127961
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7399.20.3962

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 REPLACEMENTTHROUGHOUT3MRW1.7502796126489140499.940.174430.172240.170450.20503RANDOM29.519
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]
-1.71-0.86-1.712.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.408
r_dihedral_angle_4_deg18.907
r_dihedral_angle_3_deg13.525
r_scangle_it6.154
r_dihedral_angle_1_deg5.71
r_scbond_it4.05
r_mcangle_it2.536
r_angle_refined_deg2.334
r_mcbond_it1.599
r_chiral_restr0.181
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.408
r_dihedral_angle_4_deg18.907
r_dihedral_angle_3_deg13.525
r_scangle_it6.154
r_dihedral_angle_1_deg5.71
r_scbond_it4.05
r_mcangle_it2.536
r_angle_refined_deg2.334
r_mcbond_it1.599
r_chiral_restr0.181
r_bond_refined_d0.021
r_gen_planes_refined0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1911
Nucleic Acid Atoms
Solvent Atoms229
Heterogen Atoms43

Software

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