3NDK

RB69 DNA Polymerase (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
1micro-batch vapor-diffusion6.529310% (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
2.5852.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.006α = 90
b = 120.015β = 90
c = 130.781γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2009-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.07500NSLSX29A

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
125095.30.148.53.380523767381
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)
22.07960.8791.183.2

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 3NCI2507645872811386595.230.1890.186850.22865RANDOM28.679
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]
-0.650.8-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.266
r_dihedral_angle_3_deg13.879
r_dihedral_angle_4_deg13.852
r_dihedral_angle_1_deg4.884
r_scangle_it3.347
r_scbond_it2.213
r_mcangle_it1.98
r_mcbond_it1.138
r_angle_refined_deg1.023
r_chiral_restr0.069
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.266
r_dihedral_angle_3_deg13.879
r_dihedral_angle_4_deg13.852
r_dihedral_angle_1_deg4.884
r_scangle_it3.347
r_scbond_it2.213
r_mcangle_it1.98
r_mcbond_it1.138
r_angle_refined_deg1.023
r_chiral_restr0.069
r_bond_refined_d0.007
r_gen_planes_refined0.004
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 Atoms630
Solvent Atoms875
Heterogen Atoms35

Software

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