2JG6

CRYSTAL STRUCTURE OF A 3-METHYLADENINE DNA GLYCOSYLASE I FROM STAPHYLOCOCCUS AUREUS


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.51,6 M TRISODIUM CITRATE, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
3.0459.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.46α = 90
b = 63.098β = 109.24
c = 38.47γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2006-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.75097.10.06234.526056
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)
11.71.76760.253.64.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.729.8124735132197.10.1640.1630.193RANDOM20.74
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]
-0.020.270.030.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.285
r_dihedral_angle_4_deg23.193
r_dihedral_angle_3_deg11.717
r_dihedral_angle_1_deg5.025
r_scangle_it2.782
r_scbond_it1.856
r_mcangle_it1.218
r_angle_refined_deg1.093
r_mcbond_it0.761
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.285
r_dihedral_angle_4_deg23.193
r_dihedral_angle_3_deg11.717
r_dihedral_angle_1_deg5.025
r_scangle_it2.782
r_scbond_it1.856
r_mcangle_it1.218
r_angle_refined_deg1.093
r_mcbond_it0.761
r_nbtor_refined0.307
r_nbd_refined0.196
r_symmetry_vdw_refined0.175
r_symmetry_hbond_refined0.137
r_xyhbond_nbd_refined0.116
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms1516
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing