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Pre-insertion binary complex of Dbh DNA polymerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IM4 PDB entries 1IM4 and 1K1Q experimental model PDB 1K1Q PDB entries 1IM4 and 1K1Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 PEG-3350, calcium acetate, glycerol, HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.56 51.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.416 α = 90 b = 119.416 β = 90 c = 68.274 γ = 90
Symmetry Space Group P 41 21 2
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 2006-10-21 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.9795 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 20 89.3 0.048 35.4 4.6 14027 -1
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) 1 2.6 2.64 81.4 0.314 3.4 2.9
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 PDB entries 1IM4 and 1K1Q 2.6 19.9 13804 13125 679 88.15 0.21711 0.21387 0.2162 0.27904 0.216 RANDOM 52.826
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] 3.07 3.07 -6.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.56 r_dihedral_angle_3_deg 18.777 r_dihedral_angle_4_deg 15.758 r_dihedral_angle_1_deg 5.532 r_scangle_it 1.466 r_angle_refined_deg 1.246 r_scbond_it 0.859 r_mcangle_it 0.698 r_mcbond_it 0.398 r_metal_ion_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.56 r_dihedral_angle_3_deg 18.777 r_dihedral_angle_4_deg 15.758 r_dihedral_angle_1_deg 5.532 r_scangle_it 1.466 r_angle_refined_deg 1.246 r_scbond_it 0.859 r_mcangle_it 0.698 r_mcbond_it 0.398 r_metal_ion_refined 0.311 r_nbtor_refined 0.306 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.203 r_symmetry_vdw_refined 0.202 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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 2704 Nucleic Acid Atoms 462 Solvent Atoms 110 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction HKL-2000 data scaling