3NHG

RB69 DNA Polymerase (S565G/Y567A) Ternary Complex with dTTP Opposite dG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NCIPDB ENTRY 3NCI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5293apply 7% (w/v) PEG 350 monomethyl ether (MME), 175 mM CaCl2, and 100 mM NaCacodylate (pH 6.5) to crystal Y567A/S565G: P/T:dCTP ternary complex and then soak dTTP into the crystal to replace dCTP in the ternary complex, micro-batch vapor-diffusion, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5752.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.052α = 90
b = 119.999β = 90
c = 130.382γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2010-02-27MSINGLE 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
12.55096.10.10812.24.941375397611
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.52.5995.21.14.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 3NCI2.5503937737719199495.790.188480.18550.24403RANDOM58.848
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]
0.220.28-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.752
r_dihedral_angle_4_deg17.787
r_dihedral_angle_3_deg16.349
r_dihedral_angle_1_deg5.168
r_scangle_it2.841
r_mcangle_it2.798
r_scbond_it1.843
r_mcbond_it1.679
r_angle_refined_deg1.197
r_chiral_restr0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.752
r_dihedral_angle_4_deg17.787
r_dihedral_angle_3_deg16.349
r_dihedral_angle_1_deg5.168
r_scangle_it2.841
r_mcangle_it2.798
r_scbond_it1.843
r_mcbond_it1.679
r_angle_refined_deg1.197
r_chiral_restr0.084
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 Atoms7365
Nucleic Acid Atoms630
Solvent Atoms313
Heterogen Atoms35

Software

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