☰ Navigation Tabs
Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XHX copy c of 1xhx without residues 359-394
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 100 mM sodium acetate, 200 mM ammonium acetate, 15% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.79 55.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.835 α = 90 b = 114.667 β = 94.07 c = 104.761 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2006-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.03 50 98 0.076 16.3 3.5 109968 107450 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.03 2.1 83.9 0.353 2.4 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT copy c of 1xhx without residues 359-394 2.03 41.07 104147 102064 5354 97.68 0.19128 0.18904 0.2452 0.23409 0.2836 RANDOM 12.585
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.566 r_dihedral_angle_3_deg 13.753 r_dihedral_angle_4_deg 10.536 r_dihedral_angle_1_deg 6.272 r_angle_other_deg 2.205 r_scangle_it 2.048 r_mcangle_it 2.034 r_mcbond_it 1.982 r_scbond_it 1.905 r_angle_refined_deg 1.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.566 r_dihedral_angle_3_deg 13.753 r_dihedral_angle_4_deg 10.536 r_dihedral_angle_1_deg 6.272 r_angle_other_deg 2.205 r_scangle_it 2.048 r_mcangle_it 2.034 r_mcbond_it 1.982 r_scbond_it 1.905 r_angle_refined_deg 1.171 r_nbd_other 0.215 r_symmetry_vdw_other 0.199 r_nbd_refined 0.195 r_nbtor_refined 0.188 r_mcbond_other 0.184 r_xyhbond_nbd_refined 0.14 r_symmetry_vdw_refined 0.119 r_metal_ion_refined 0.111 r_symmetry_hbond_refined 0.107 r_nbtor_other 0.085 r_chiral_restr 0.07 r_bond_refined_d 0.012 r_bond_other_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 9367 Nucleic Acid Atoms 1431 Solvent Atoms 969 Heterogen Atoms 230
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling