2XY6

Crystal structure of a salicylic aldehyde basepair in complex with fragment DNA polymerase I from Bacillus stearothermophilus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U45PDB ENTRY 1U45

Crystallization

Crystal Properties
Matthews coefficientSolvent content
3.2862.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.235α = 90
b = 93.127β = 90
c = 105.505γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2009-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
12.35099.90.0715.23.8393342
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)
12.32.421000.43.63.8

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 1U452.345.2837312196499.920.215190.213130.25417RANDOM23.277
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]
2.14-1.22-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.323
r_dihedral_angle_4_deg16.436
r_dihedral_angle_3_deg14.63
r_dihedral_angle_1_deg5.6
r_scangle_it3.065
r_scbond_it1.929
r_angle_refined_deg1.371
r_mcangle_it1.162
r_angle_other_deg0.907
r_mcbond_it0.601
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.323
r_dihedral_angle_4_deg16.436
r_dihedral_angle_3_deg14.63
r_dihedral_angle_1_deg5.6
r_scangle_it3.065
r_scbond_it1.929
r_angle_refined_deg1.371
r_mcangle_it1.162
r_angle_other_deg0.907
r_mcbond_it0.601
r_mcbond_other0.136
r_chiral_restr0.075
r_bond_refined_d0.013
r_bond_other_d0.006
r_gen_planes_refined0.005
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4577
Nucleic Acid Atoms403
Solvent Atoms158
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing