3EP8

Human AdoMetDC E178Q mutant complexed with S-Adenosylmethionine methyl ester and no putrescine bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1I7B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829516% PEG 8000, 100 mM Tris, 10 mM DTT, pH 8.0, vapor diffusion, hanging drop, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2645.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.146α = 90
b = 51.073β = 105.39
c = 68.947γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9795APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.975098.60.080.0815.0053.1235892300111.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.972.0491.10.2380.2383.42.52170

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 REPLACEMENTTHROUGHOUT1I7B1.9733.242358923001110695.90.2090.2090.2090.237RANDOM29.257
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]
5.23-1.981.02-6.25
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.4
c_scangle_it2.9
c_mcangle_it2.26
c_scbond_it2.01
c_angle_deg1.6
c_mcbond_it1.39
c_improper_angle_d1.38
c_bond_d0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2409
Nucleic Acid Atoms
Solvent Atoms206
Heterogen Atoms32

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing