3SCX

RB69 DNA Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the Presence of Ca2+


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH VAPOR DIFFUSION6.5293.15150 mM calcium chloride, 1% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, MICROBATCH VAPOR DIFFUSION, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.5752.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.022α = 90
b = 119.333β = 90
c = 130.663γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDADSC QUANTUM 315mirrors2007-08-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.9795APS24-ID-E

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
12.351001000.1689.236.749563495632145
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.431001.086.64897

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1IG92.3588.044698346983250799.790.216270.216270.214040.25875RANDOM43.388
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]
5.29-0.56-4.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.75
r_dihedral_angle_3_deg16.019
r_dihedral_angle_4_deg14.985
r_dihedral_angle_1_deg5.299
r_scangle_it2.713
r_scbond_it1.622
r_mcangle_it1.281
r_angle_refined_deg1.097
r_mcbond_it0.639
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.75
r_dihedral_angle_3_deg16.019
r_dihedral_angle_4_deg14.985
r_dihedral_angle_1_deg5.299
r_scangle_it2.713
r_scbond_it1.622
r_mcangle_it1.281
r_angle_refined_deg1.097
r_mcbond_it0.639
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7359
Nucleic Acid Atoms630
Solvent Atoms345
Heterogen Atoms32

Software

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