1Q9X

Crystal structure of Enterobacteria phage RB69 gp43 DNA polymerase complexed with tetrahydrofuran containing DNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1CLQPDB ENTRY 1CLQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5298PEG 350MME, Calcium chloride, Tris-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
2.8957.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.948α = 90
b = 122.237β = 96.85
c = 165.358γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X26CNSLSX26C

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
12.694794.70.11319.14.8137338
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)
12.692.873.30.4341.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1CLQ2.6947142376130465684194.70.218790.215120.2879RANDOM22.067
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]
-2.450.022.280.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.509
r_scangle_it2.295
r_angle_refined_deg1.535
r_scbond_it1.456
r_mcangle_it0.819
r_mcbond_it0.417
r_metal_ion_refined0.233
r_nbd_refined0.229
r_symmetry_vdw_refined0.229
r_symmetry_hbond_refined0.212
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.509
r_scangle_it2.295
r_angle_refined_deg1.535
r_scbond_it1.456
r_mcangle_it0.819
r_mcbond_it0.417
r_metal_ion_refined0.233
r_nbd_refined0.229
r_symmetry_vdw_refined0.229
r_symmetry_hbond_refined0.212
r_xyhbond_nbd_refined0.189
r_chiral_restr0.106
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_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 Atoms29460
Nucleic Acid Atoms2532
Solvent Atoms535
Heterogen Atoms229

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing