3S6I

Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (Mag1) in complex with abasic-DNA.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52940.1 M MES (pH 6.5), 20% (w/v) PEG 8K and 2.4% (v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.7955.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.317α = 90
b = 112.298β = 99.55
c = 61.113γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARMOSAIC 225 mm CCD2009-02-16MSINGLE WAVELENGTH
21x-ray110CCDMARMOSAIC 300 mm CCD2009-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM0.9792APS22-BM
2SYNCHROTRONAPS BEAMLINE 21-ID-D0.97872APS21-ID-D

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
1,22.2829.199.60.10911.54.83223132231-3-340.8
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)
1,22.282.3898.10.4042.53.43176

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (F)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 DIFFRACTIONSAD2.2829.11.353219932188163197.290.23620.18690.18490.2254random
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]
-7.17521.0957-2.35529.5304
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d21.87
f_angle_d1.185
f_chiral_restr0.068
f_bond_d0.008
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3184
Nucleic Acid Atoms845
Solvent Atoms112
Heterogen Atoms2

Software

Software
Software NamePurpose
HKL-2000data collection
SHARPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling