3NE6

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.52937% (w/v) PEG 350 monomethyl ether (MME), 175 mM CaCl2, 100 mM NaCacodylate (pH 6.5), micro-batch vapor-diffusion, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5852.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.135α = 90
b = 119.783β = 90
c = 130.652γ = 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 X29A1.10000NSLSX29A

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
125099.70.08318.14.68020779966131.5
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)
22.0797.80.7811.64.37743

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 3NCI2.00149.317617775880400999.610.185620.183520.22568RANDOM37.096
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]
-2.422.45-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.212
r_dihedral_angle_4_deg14.859
r_dihedral_angle_3_deg14.207
r_dihedral_angle_1_deg5.011
r_scangle_it3.591
r_scbond_it2.407
r_mcangle_it2.097
r_mcbond_it1.226
r_angle_refined_deg1.055
r_chiral_restr0.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.212
r_dihedral_angle_4_deg14.859
r_dihedral_angle_3_deg14.207
r_dihedral_angle_1_deg5.011
r_scangle_it3.591
r_scbond_it2.407
r_mcangle_it2.097
r_mcbond_it1.226
r_angle_refined_deg1.055
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7365
Nucleic Acid Atoms630
Solvent Atoms757
Heterogen Atoms33

Software

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