6W13

Human 8-oxoguanine glycosylase interrogating fully intrahelical oxoG lesion DNA


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293100 mM sodium cacodylate, pH 6.1, 200 mM MgOAc, and 17 % polyethylene glycol 8000
Crystal Properties
Matthews coefficientSolvent content
3.1665.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.707α = 90
b = 90.707β = 90
c = 210.803γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.9792APS24-ID-E

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
12.3845.3599.90.1241710.521460
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)
12.382.511.25

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 REPLACEMENTTHROUGHOUT1EBM2.3845.3520290109899.920.21660.21370.2711RANDOM52.078
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]
0.450.220.45-1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.845
r_dihedral_angle_4_deg16.552
r_dihedral_angle_3_deg12.912
r_dihedral_angle_1_deg5.659
r_angle_other_deg2.59
r_angle_refined_deg1.361
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_gen_planes_other0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.845
r_dihedral_angle_4_deg16.552
r_dihedral_angle_3_deg12.912
r_dihedral_angle_1_deg5.659
r_angle_other_deg2.59
r_angle_refined_deg1.361
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2484
Nucleic Acid Atoms267
Solvent Atoms85
Heterogen Atoms28

Software

Software
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data processing
HKL-2000data scaling