2XY7

Crystal structure of a salicylic aldehyde base in the pre-insertion site of 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
3.2762.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.037α = 90
b = 94.022β = 90
c = 106.711γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2010-03-28MSINGLE 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
13.0546.4990.159.53.4168292
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)
13.053.2199.10.5333.5

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 1U453.0543.021595983698.540.238530.236180.28373RANDOM30.531
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]
7.43-3.36-4.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.644
r_dihedral_angle_4_deg19.342
r_dihedral_angle_3_deg19.25
r_dihedral_angle_1_deg4.833
r_angle_other_deg4.121
r_scangle_it2.277
r_scbond_it1.223
r_angle_refined_deg1.121
r_mcangle_it0.409
r_mcbond_it0.197
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.644
r_dihedral_angle_4_deg19.342
r_dihedral_angle_3_deg19.25
r_dihedral_angle_1_deg4.833
r_angle_other_deg4.121
r_scangle_it2.277
r_scbond_it1.223
r_angle_refined_deg1.121
r_mcangle_it0.409
r_mcbond_it0.197
r_chiral_restr0.055
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_gen_planes_other0.003
r_bond_other_d
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_mcbond_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 Atoms4497
Nucleic Acid Atoms423
Solvent Atoms8
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing