3LZJ

RB69 DNA Polymerase (Y567A) ternary complex with dCTP Opposite 7,8-Dihydro-8-oxoguanine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1micro-batch vapor-diffusion6.5293.15150 mM CaCl2, 14%(w/v) PEG 350 monomethyl ether (MME), and 100 mM Na Cacodylate (pH 6.5), micro-batch vapor-diffusion, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.4950.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.394α = 90
b = 121.089β = 90
c = 122.857γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDADSC QUANTUM 315mirrors2009-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.075NSLSX29A

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
12.055090.70.07316.53.8655941.03
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)
12.052.1270.20.9621.032.3

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 DIFFRACTIONTHROUGHOUT2.0538.8162176331790.780.206960.204620.25065RANDOM11.084
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]
3.293.61-6.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.694
r_dihedral_angle_3_deg16.712
r_dihedral_angle_4_deg15.473
r_dihedral_angle_1_deg5.511
r_scangle_it3.984
r_scbond_it2.782
r_mcangle_it2.296
r_mcbond_it1.437
r_angle_refined_deg1.258
r_chiral_restr0.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.694
r_dihedral_angle_3_deg16.712
r_dihedral_angle_4_deg15.473
r_dihedral_angle_1_deg5.511
r_scangle_it3.984
r_scbond_it2.782
r_mcangle_it2.296
r_mcbond_it1.437
r_angle_refined_deg1.258
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7367
Nucleic Acid Atoms634
Solvent Atoms568
Heterogen Atoms32

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling