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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 9.5 293 100 mM CHES, 15-20% PEG 8000, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.44 49.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.922 α = 90 b = 78.199 β = 90 c = 157.813 γ = 90
Symmetry Space Group P 21 21 21
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 1.00003 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 2.2 50 97 0.166 8.9 4.8 37873 36737 -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) 2.2 2.28 83.7 0.85 1.2 2.5
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 2.2 40.42 37856 33015 3649 96.86 0.19732 0.19128 0.2169 0.25291 0.2723 RANDOM 14.113
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] 0.41 -0.22 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.64 r_dihedral_angle_4_deg 16.138 r_dihedral_angle_3_deg 14.314 r_dihedral_angle_1_deg 6.637 r_angle_other_deg 2.144 r_scangle_it 1.883 r_mcangle_it 1.776 r_scbond_it 1.685 r_mcbond_it 1.61 r_angle_refined_deg 1.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.64 r_dihedral_angle_4_deg 16.138 r_dihedral_angle_3_deg 14.314 r_dihedral_angle_1_deg 6.637 r_angle_other_deg 2.144 r_scangle_it 1.883 r_mcangle_it 1.776 r_scbond_it 1.685 r_mcbond_it 1.61 r_angle_refined_deg 1.271 r_nbd_other 0.212 r_mcbond_other 0.196 r_nbd_refined 0.189 r_nbtor_refined 0.188 r_symmetry_vdw_other 0.165 r_xyhbond_nbd_refined 0.151 r_symmetry_hbond_refined 0.136 r_nbtor_other 0.082 r_chiral_restr 0.073 r_symmetry_vdw_refined 0.062 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_xyhbond_nbd_other 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 4680 Nucleic Acid Atoms 505 Solvent Atoms 357 Heterogen Atoms 55
Software Software Software Name Purpose CBASS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling