3BUC

X-ray structure of human ABH2 bound to dsDNA with Mn(II) and 2KG


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52778% PEG 8000, 0.1M sodium chloride, 0.05M magnesium chloride, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.1961.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.91α = 90
b = 77.91β = 90
c = 226.558γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002007-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9717APS19-BM

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
12.595098.90.04922.36.21337313373
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)
12.592.631000.6772.15.9649

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 REPLACEMENTTHROUGHOUT2.59201239465497.420.25040.248480.28673RANDOM46.994
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]
-1.67-0.83-1.672.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.165
r_dihedral_angle_3_deg15.343
r_dihedral_angle_4_deg14.424
r_dihedral_angle_1_deg5.71
r_scangle_it1.354
r_angle_refined_deg1.279
r_scbond_it0.777
r_mcangle_it0.48
r_nbtor_refined0.305
r_mcbond_it0.265
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.165
r_dihedral_angle_3_deg15.343
r_dihedral_angle_4_deg14.424
r_dihedral_angle_1_deg5.71
r_scangle_it1.354
r_angle_refined_deg1.279
r_scbond_it0.777
r_mcangle_it0.48
r_nbtor_refined0.305
r_mcbond_it0.265
r_nbd_refined0.195
r_symmetry_vdw_refined0.195
r_xyhbond_nbd_refined0.166
r_symmetry_hbond_refined0.129
r_chiral_restr0.072
r_bond_refined_d0.007
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 Atoms1617
Nucleic Acid Atoms526
Solvent Atoms37
Heterogen Atoms15

Software

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