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Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with duplex DNA 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 7.5 0.1 M HEPES pH 7.5, 2.0 M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.87 57.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.34 α = 90 b = 93.587 β = 90 c = 104.618 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 2011-02-18 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 2.45 30 92.1 0.112 7.2 2.7 32689 30107
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 2.45 2.54 79 0.386 1.9 2 3240
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB 3HT3 2.45 30 32689 26904 3027 91.5 0.22875 0.22875 0.22225 0.28568 0.2642 RANDOM 39.568
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] 4.75 -3.35 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.212 r_dihedral_angle_4_deg 25.335 r_dihedral_angle_3_deg 21.337 r_dihedral_angle_1_deg 7.253 r_scangle_it 3.301 r_scbond_it 2.062 r_angle_refined_deg 1.829 r_mcangle_it 1.263 r_mcbond_it 0.654 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.212 r_dihedral_angle_4_deg 25.335 r_dihedral_angle_3_deg 21.337 r_dihedral_angle_1_deg 7.253 r_scangle_it 3.301 r_scbond_it 2.062 r_angle_refined_deg 1.829 r_mcangle_it 1.263 r_mcbond_it 0.654 r_chiral_restr 0.112 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 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 4649 Nucleic Acid Atoms 489 Solvent Atoms 65 Heterogen Atoms 10
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling