5CIX

Structure of the complex of type 1 Ribosome inactivating protein with triethanolamine at 1.88 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JTP 

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
2.346.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.262α = 90
b = 130.262β = 90
c = 38.158γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCH2015-02-15MSINGLE 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
11.8832.5799.50.0740.01852.119516
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.9196.60.3352.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4JTP1.8832.571782895295.640.16860.1660.2178RANDOM44.053
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]
0.040.020.04-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.069
r_dihedral_angle_4_deg18.393
r_dihedral_angle_3_deg13.24
r_dihedral_angle_1_deg5.81
r_mcangle_it4.511
r_mcbond_other3.444
r_mcbond_it3.442
r_angle_refined_deg1.794
r_angle_other_deg0.887
r_chiral_restr0.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.069
r_dihedral_angle_4_deg18.393
r_dihedral_angle_3_deg13.24
r_dihedral_angle_1_deg5.81
r_mcangle_it4.511
r_mcbond_other3.444
r_mcbond_it3.442
r_angle_refined_deg1.794
r_angle_other_deg0.887
r_chiral_restr0.103
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1910
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata collection
SCALEPACKdata scaling
MOLREPmodel building
PDB_EXTRACTdata extraction
SCALEPACKdata reduction
Cootphasing