4EMF

Crystal structure of the complex of type I Ribosome inactivating protein in complex with 7n-methyl-8-hydroguanosine-5-p-diphosphate at 1.77 A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3S9Q 

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
2.3848.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.87α = 90
b = 129.87β = 90
c = 39.78γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHmirror2010-10-21MSINGLE 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
11.7764.9399.90.06313.22302623026
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)
11.771.8799.60.5652.4

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 REPLACEMENTTHROUGHOUT3S9Q1.77332302623026123899.930.174530.17120.16820.22772RANDOM30.163
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]
-1.83-0.91-1.832.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.677
r_dihedral_angle_4_deg18.523
r_dihedral_angle_3_deg13.514
r_dihedral_angle_1_deg5.733
r_scangle_it5.195
r_scbond_it3.449
r_mcangle_it2.131
r_angle_refined_deg2.064
r_mcbond_it1.268
r_chiral_restr0.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.677
r_dihedral_angle_4_deg18.523
r_dihedral_angle_3_deg13.514
r_dihedral_angle_1_deg5.733
r_scangle_it5.195
r_scbond_it3.449
r_mcangle_it2.131
r_angle_refined_deg2.064
r_mcbond_it1.268
r_chiral_restr0.144
r_bond_refined_d0.023
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1911
Nucleic Acid Atoms
Solvent Atoms240
Heterogen Atoms55

Software

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