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Phi29 DNA polymerase complexed with primer-template DNA (post-translocation binary complex)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XHX copy c of 1XHX without residues 358-394
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 100 mM Tris-HCl, 20% PEG 10000, 200 mM magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.73 54.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 216.633 α = 90 b = 146.292 β = 117.93 c = 115.054 γ = 90
Symmetry Space Group C 1 2 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 2005-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.10000 NSLS X25
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 2.6 50 98.4 0.152 5.8 2.1 97325 95762 -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) 2.6 2.69 95.1 0.773 1 2.1
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 358-394 2.6 45.22 97325 85919 9703 98.32 0.22452 0.21872 0.2373 0.27524 0.2894 RANDOM 22.349
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] 0.15 0.26 0.01 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.875 r_dihedral_angle_3_deg 17.311 r_dihedral_angle_4_deg 16.026 r_dihedral_angle_1_deg 6.778 r_scangle_it 1.894 r_mcangle_it 1.491 r_scbond_it 1.344 r_angle_refined_deg 1.239 r_mcbond_it 1.188 r_angle_other_deg 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.875 r_dihedral_angle_3_deg 17.311 r_dihedral_angle_4_deg 16.026 r_dihedral_angle_1_deg 6.778 r_scangle_it 1.894 r_mcangle_it 1.491 r_scbond_it 1.344 r_angle_refined_deg 1.239 r_mcbond_it 1.188 r_angle_other_deg 0.87 r_symmetry_vdw_refined 0.294 r_symmetry_hbond_refined 0.287 r_symmetry_vdw_other 0.232 r_mcbond_other 0.221 r_nbd_refined 0.207 r_nbtor_refined 0.193 r_nbd_other 0.185 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.083 r_nbtor_other 0.083 r_xyhbond_nbd_other 0.046 r_bond_refined_d 0.011 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined 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 18487 Nucleic Acid Atoms 1207 Solvent Atoms 89 Heterogen Atoms
Software Software Software Name Purpose CBASS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling