3NAE

RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite Guanidinohydantoin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IG9PDB ENTRY 1IG9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1micro-batch vapor-diffusion6.529315%(w/v) PEG 350 monomethyl ether (MME), 150 mM CaCl2, and 100 mM NaCacodylate (pH 6.5), micro-batch vapor-diffusion, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5752.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.013α = 90
b = 119.783β = 90
c = 130.727γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-03-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.10000NSLSX25

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
125093.70.07814.34.574483697941
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)
22.0775.810.9583.25982

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 1IG92.00335.24175863697943673920.195960.194070.23092RANDOM27.263
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]
-0.730.9-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.029
r_dihedral_angle_3_deg14.201
r_dihedral_angle_4_deg13.422
r_dihedral_angle_1_deg4.889
r_scangle_it3.701
r_scbond_it2.422
r_mcangle_it2.182
r_mcbond_it1.231
r_angle_refined_deg1.106
r_chiral_restr0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.029
r_dihedral_angle_3_deg14.201
r_dihedral_angle_4_deg13.422
r_dihedral_angle_1_deg4.889
r_scangle_it3.701
r_scbond_it2.422
r_mcangle_it2.182
r_mcbond_it1.231
r_angle_refined_deg1.106
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7367
Nucleic Acid Atoms630
Solvent Atoms704
Heterogen Atoms34

Software

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