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Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with self complementary DNA, Se-dGTP and Calcium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HT3 PDB 3HT3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 0. M Bis-Tris, pH 6.5, 2.0 M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 3.01 59.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.051 α = 90 b = 93.545 β = 90 c = 105.543 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 Mirrors 2011-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 1.0000 ALS 12.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.85 70.01 96.8 0.099 11.5 3.9 75057 72655
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 90.1 0.383 1.9 2.5 7408
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 (All) 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 PDB 3HT3 1.85 70.01 75057 68796 3635 96.58 0.21644 0.21644 0.21407 0.2153 0.26307 0.2663 RANDOM 25.043
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] 1.7 -0.87 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.413 r_dihedral_angle_4_deg 21.274 r_dihedral_angle_3_deg 17.309 r_dihedral_angle_1_deg 6.253 r_scangle_it 4.514 r_scbond_it 2.859 r_angle_refined_deg 1.836 r_mcangle_it 1.695 r_mcbond_it 0.922 r_chiral_restr 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.413 r_dihedral_angle_4_deg 21.274 r_dihedral_angle_3_deg 17.309 r_dihedral_angle_1_deg 6.253 r_scangle_it 4.514 r_scbond_it 2.859 r_angle_refined_deg 1.836 r_mcangle_it 1.695 r_mcbond_it 0.922 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4659 Nucleic Acid Atoms 376 Solvent Atoms 209 Heterogen Atoms 67
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling