3HPO

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus Y714S mutant bound to G:T mismatch


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L3UPDB entry 1L3U

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.829050% Saturated ammonium sulfate, 0.1M MES, 2.5% v/v Methylpentanediol, 10mM Magnesium sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
3.160.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.21α = 90
b = 93.73β = 90
c = 105.51γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.00000APS22-BM

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
11.7445.9890.60.08410.6659224183554-329.055
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)
11.741.8577.90.4092.94.511929

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 REPLACEMENTTHROUGHOUTPDB entry 1L3U1.7545.988355441781000.2030.2010.241RANDOM25.3
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.559
r_dihedral_angle_4_deg14.502
r_dihedral_angle_3_deg13.839
r_dihedral_angle_1_deg5.022
r_scangle_it2.99
r_scbond_it1.82
r_angle_refined_deg1.17
r_mcangle_it1.134
r_mcbond_it0.584
r_chiral_restr0.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.559
r_dihedral_angle_4_deg14.502
r_dihedral_angle_3_deg13.839
r_dihedral_angle_1_deg5.022
r_scangle_it2.99
r_scbond_it1.82
r_angle_refined_deg1.17
r_mcangle_it1.134
r_mcbond_it0.584
r_chiral_restr0.079
r_bond_refined_d0.008
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4649
Nucleic Acid Atoms387
Solvent Atoms724
Heterogen Atoms58

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
XDSdata reduction
PHASERphasing