1Q9Y

CRYSTAL STRUCTURE OF ENTEROBACTERIA PHAGE RB69 GP43 DNA POLYMERASE COMPLEXED WITH 8-OXOGUANOSINE CONTAINING DNA


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298PEG 350MME, Calcium chloride, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.6553.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.822α = 90
b = 118.565β = 90
c = 127.224γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCUSTOM-MADE2002-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X25NSLSX25

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.85099.90.11611.07774.530441
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.82.91000.6161.84

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 1IG92.846.0628854153399.520.207260.203890.27067RANDOM19.234
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]
-1.53-0.221.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.511
r_scangle_it2.818
r_angle_refined_deg1.865
r_scbond_it1.732
r_mcangle_it1.04
r_angle_other_deg0.975
r_mcbond_it0.548
r_metal_ion_refined0.33
r_symmetry_hbond_refined0.262
r_nbd_refined0.239
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.511
r_scangle_it2.818
r_angle_refined_deg1.865
r_scbond_it1.732
r_mcangle_it1.04
r_angle_other_deg0.975
r_mcbond_it0.548
r_metal_ion_refined0.33
r_symmetry_hbond_refined0.262
r_nbd_refined0.239
r_nbd_other0.236
r_symmetry_vdw_other0.225
r_xyhbond_nbd_refined0.188
r_symmetry_vdw_refined0.122
r_nbtor_other0.093
r_chiral_restr0.091
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7356
Nucleic Acid Atoms652
Solvent Atoms84
Heterogen Atoms31

Software

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