2XO7

Crystal structure of a dA:O-allylhydroxylamine-dC basepair in complex with fragment DNA polymerase I from Bacillus stearothermophilus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.850-55% (NH4)2SO4 3-3.5% MPD 100MM MES, PH 5.8 10MG/ML PROTEIN/DNA 1:3
Crystal Properties
Matthews coefficientSolvent content
3.2666.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.478α = 90
b = 93.636β = 90
c = 105.091γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2009-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DASLSX06DA

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
12.8543.7499.70.08313.33.6207042
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)
12.8531000.3993.33.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1U452.8543.7419570104799.40.2160.2150.245RANDOM33.17
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]
4.92-3.45-1.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.473
r_dihedral_angle_4_deg18.326
r_dihedral_angle_3_deg18.074
r_dihedral_angle_1_deg4.878
r_scangle_it2.917
r_scbond_it1.675
r_angle_refined_deg1.384
r_mcangle_it0.967
r_angle_other_deg0.887
r_mcbond_it0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.473
r_dihedral_angle_4_deg18.326
r_dihedral_angle_3_deg18.074
r_dihedral_angle_1_deg4.878
r_scangle_it2.917
r_scbond_it1.675
r_angle_refined_deg1.384
r_mcangle_it0.967
r_angle_other_deg0.887
r_mcbond_it0.47
r_mcbond_other0.089
r_chiral_restr0.069
r_bond_refined_d0.013
r_bond_other_d0.006
r_gen_planes_refined0.005
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 Atoms4633
Nucleic Acid Atoms428
Solvent Atoms7
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing