2PYJ

Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6293100 mM sodium acetate, 200 mM ammonium acetate, 15% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7955.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.835α = 90
b = 114.667β = 94.07
c = 104.761γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-08-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-CAPS24-ID-C

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
12.0350980.07616.33.5109968107450-3
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)
2.032.183.90.3532.42.3

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 REPLACEMENTTHROUGHOUTcopy c of 1xhx without residues 359-3942.0341.07104147102064535497.680.191280.189040.23409RANDOM12.585
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.566
r_dihedral_angle_3_deg13.753
r_dihedral_angle_4_deg10.536
r_dihedral_angle_1_deg6.272
r_angle_other_deg2.205
r_scangle_it2.048
r_mcangle_it2.034
r_mcbond_it1.982
r_scbond_it1.905
r_angle_refined_deg1.171
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.566
r_dihedral_angle_3_deg13.753
r_dihedral_angle_4_deg10.536
r_dihedral_angle_1_deg6.272
r_angle_other_deg2.205
r_scangle_it2.048
r_mcangle_it2.034
r_mcbond_it1.982
r_scbond_it1.905
r_angle_refined_deg1.171
r_nbd_other0.215
r_symmetry_vdw_other0.199
r_nbd_refined0.195
r_nbtor_refined0.188
r_mcbond_other0.184
r_xyhbond_nbd_refined0.14
r_symmetry_vdw_refined0.119
r_metal_ion_refined0.111
r_symmetry_hbond_refined0.107
r_nbtor_other0.085
r_chiral_restr0.07
r_bond_refined_d0.012
r_bond_other_d0.003
r_gen_planes_refined0.003
r_gen_planes_other0.002
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9367
Nucleic Acid Atoms1431
Solvent Atoms969
Heterogen Atoms230

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling