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Mechanism of Template-Independent Nucleotide Incorporation Catalyzed by a Template-Dependent DNA Polymerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JX4 PDB Entry: 1JX4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 10% PEG3350, 0.1 M Calcium acetate, 0.1 M hepes pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.69 54.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.057 α = 90 b = 101.857 β = 90 c = 52.38 γ = 90
Symmetry Space Group P 21 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 173 IMAGE PLATE RIGAKU RAXIS IV mirrors 2002-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.05 30 97.5 0.063 16.7 32881
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 2.05 2.09 93.7 0.34 1570
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 Entry: 1JX4 2.05 26.73 32833 954 100 0.232 0.23 0.2191 0.284 0.2716 RANDOM 45.315
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] 2.66 -1.89 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.88 r_dihedral_angle_3_deg 14.592 r_dihedral_angle_4_deg 12.457 r_dihedral_angle_1_deg 4.618 r_scangle_it 3.114 r_scbond_it 2.5 r_mcangle_it 1.372 r_angle_refined_deg 1.303 r_mcbond_it 1.231 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.88 r_dihedral_angle_3_deg 14.592 r_dihedral_angle_4_deg 12.457 r_dihedral_angle_1_deg 4.618 r_scangle_it 3.114 r_scbond_it 2.5 r_mcangle_it 1.372 r_angle_refined_deg 1.303 r_mcbond_it 1.231 r_nbtor_refined 0.306 r_nbd_refined 0.223 r_symmetry_hbond_refined 0.207 r_xyhbond_nbd_refined 0.176 r_symmetry_vdw_refined 0.167 r_metal_ion_refined 0.148 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2788 Nucleic Acid Atoms 568 Solvent Atoms 240 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS refinement DENZO data reduction PDB_EXTRACT data extraction HKL-2000 data collection CNS phasing