3GA6

Mth0212 in complex with two DNA helices


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.6293reservoir solution: 5% (w/v) PEG 8000, 200mM KCl, 10 mM MgCl2, 50mM MES pH 5.6, 2mM DTT; complex solution: 245mM NaCl, 8mM HEPES-KOH pH 7.6, 2mM MgCl2, 3mM DTT , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthew coefficientSolvent content
2.4549.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.834α = 90
b = 126.655β = 93.14
c = 54.826γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91800BESSY14.2

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
11.8985095.80.07522.26.75627228
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.8981.9772.20.6071.84.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3FZI1.89833.7090.0652596332689.390.1580.1550.203in (40) thin shells (using DATAMAN), 6.0 %36.76
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]
-3.515-6.4945.798-3.82
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d22.34
f_angle_d1.359
f_chiral_restr0.088
f_bond_d0.008
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4249
Nucleic Acid Atoms901
Solvent Atoms354
Heterogen Atoms125

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing