3MY6

Crystal Structure of the complex of type 1 ribosome inactivating protein with 7-methylguanine at 2.65 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AHA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17298PEG, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4449.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.428α = 90
b = 131.428β = 90
c = 39.808γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray292IMAGE PLATEMAR scanner 345 mm plateMIRROR2009-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.6520100735553.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.652.75100

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1AHA2.6519.767355735540199.20.1740.1740.21RANDOM42.4
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]
-8.73-0.87-8.7317.47
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.3
c_scangle_it2.82
c_mcangle_it2.11
c_scbond_it1.85
c_angle_deg1.7
c_mcbond_it1.25
c_improper_angle_d0.97
c_bond_d0.01
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.3
c_scangle_it2.82
c_mcangle_it2.11
c_scbond_it1.85
c_angle_deg1.7
c_mcbond_it1.25
c_improper_angle_d0.97
c_bond_d0.01
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1909
Nucleic Acid Atoms
Solvent Atoms114
Heterogen Atoms40

Software

Software
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
CNSrefinement
AUTOMARdata reduction
SCALEPACKdata scaling