1OE6

Xenopus SMUG1, an anti-mutator uracil-DNA Glycosylase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherNATIVE STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.8856.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.969α = 90
b = 86.518β = 118.53
c = 78.456γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2002-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
12.655099.40.0926.34.120624
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)
12.652.79960.4381.63.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTNATIVE STRUCTURE2.6569.0119561106399.40.1570.1540.218RANDOM44.55
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]
1.722.3-0.080.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg9.143
r_scangle_it8.203
r_scbond_it5.112
r_angle_refined_deg4.073
r_angle_other_deg3.405
r_mcangle_it3.316
r_mcbond_it1.836
r_nbd_refined0.315
r_nbd_other0.298
r_xyhbond_nbd_refined0.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg9.143
r_scangle_it8.203
r_scbond_it5.112
r_angle_refined_deg4.073
r_angle_other_deg3.405
r_mcangle_it3.316
r_mcbond_it1.836
r_nbd_refined0.315
r_nbd_other0.298
r_xyhbond_nbd_refined0.296
r_symmetry_vdw_other0.277
r_chiral_restr0.212
r_symmetry_vdw_refined0.162
r_nbtor_other0.127
r_symmetry_hbond_refined0.095
r_bond_refined_d0.051
r_gen_planes_refined0.018
r_gen_planes_other0.012
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3869
Nucleic Acid Atoms478
Solvent Atoms110
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling