3BKZ

X-ray structure of E coli AlkB crosslinked to dsDNA in the active site


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527720% PEG 5000, 0.1M sodium chloride, 25 mM magnesium chloride, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3347.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.397α = 90
b = 75.507β = 105.45
c = 46.788γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-D0.97APS14-BM-D

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
11.595098.60.059163.73660736607
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)
11.591.6587.30.36622.4

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.652031663166399.860.188820.187560.21236RANDOM22.876
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]
-0.69-0.13-0.41.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.848
r_dihedral_angle_3_deg11.434
r_dihedral_angle_4_deg11.354
r_dihedral_angle_1_deg5.764
r_angle_refined_deg1.04
r_scangle_it0.984
r_scbond_it0.618
r_mcangle_it0.53
r_mcbond_it0.365
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.848
r_dihedral_angle_3_deg11.434
r_dihedral_angle_4_deg11.354
r_dihedral_angle_1_deg5.764
r_angle_refined_deg1.04
r_scangle_it0.984
r_scbond_it0.618
r_mcangle_it0.53
r_mcbond_it0.365
r_nbtor_refined0.297
r_nbd_refined0.172
r_symmetry_vdw_refined0.099
r_xyhbond_nbd_refined0.094
r_symmetry_hbond_refined0.063
r_chiral_restr0.061
r_bond_refined_d0.005
r_gen_planes_refined0.003
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1570
Nucleic Acid Atoms529
Solvent Atoms292
Heterogen Atoms11

Software

Software
Software NamePurpose
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling