6UR2

DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template and primer containing an N3'-> P5' linkage


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L5U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729110mM MgCl2, 0.8 M Succinic acid pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.8261.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.197α = 90
b = 93.679β = 90
c = 107.14γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray99CCDMAR CCD 130 mm2018-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21ALS8.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.275099.90.120.1290.0460.99117.9839951
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.282.361000.5080.5430.1920.9864.78

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1L5U2.2740.8537883197099.080.23130.2290.2767RANDOM42.616
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]
0.010.04-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.139
r_dihedral_angle_4_deg20.265
r_dihedral_angle_3_deg17.207
r_dihedral_angle_1_deg6.967
r_angle_refined_deg1.55
r_angle_other_deg1.281
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.139
r_dihedral_angle_4_deg20.265
r_dihedral_angle_3_deg17.207
r_dihedral_angle_1_deg6.967
r_angle_refined_deg1.55
r_angle_other_deg1.281
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4649
Nucleic Acid Atoms449
Solvent Atoms100
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing