3BTY | pdb_00003bty

Crystal structure of human ABH2 bound to dsDNA containing 1meA through cross-linking away from active site


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
3.1961.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.915α = 90
b = 77.915β = 90
c = 226.04γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BMAPS19-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
12.355095.60.0523014.51706217062
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)
12.352.391000.6752.213.3860

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.35201615387496.050.225180.223370.220.258930.25RANDOM50.67
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]
-1.76-0.88-1.762.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.429
r_dihedral_angle_3_deg12.703
r_dihedral_angle_4_deg12.192
r_dihedral_angle_1_deg5.603
r_scangle_it1.184
r_angle_refined_deg1.116
r_scbond_it0.688
r_mcangle_it0.44
r_nbtor_refined0.293
r_mcbond_it0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.429
r_dihedral_angle_3_deg12.703
r_dihedral_angle_4_deg12.192
r_dihedral_angle_1_deg5.603
r_scangle_it1.184
r_angle_refined_deg1.116
r_scbond_it0.688
r_mcangle_it0.44
r_nbtor_refined0.293
r_mcbond_it0.25
r_nbd_refined0.165
r_symmetry_vdw_refined0.138
r_xyhbond_nbd_refined0.134
r_symmetry_hbond_refined0.108
r_chiral_restr0.063
r_bond_refined_d0.006
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 Atoms124
Heterogen Atoms4

Software

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