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Uracil Recognition in Archaeal DNA Polymerases Captured by X-ray Crystallography.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TGO PDB ENTRY 1TGO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.3 0.2M TRIPOTASSIUM CITRATE PH8.3, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 4.5 76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.7 α = 90 b = 161.91 β = 90 c = 221.82 γ = 90
Symmetry Space Group I 2 2 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 SI (111) DOUBLE CRYSTAL MONOCHROMATOR. KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 2.78 30 98.7 0.1 11.1 3.5 45193
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 2.78 2.85 98.9 0.44 2.2 3.6
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 1TGO 2.78 67.73 42895 2296 98.3 0.229 0.227 0.2241 0.264 0.2594 RANDOM 52.83
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] -5.18 4.01 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.104 r_dihedral_angle_4_deg 22.26 r_dihedral_angle_3_deg 19.83 r_dihedral_angle_1_deg 6.219 r_scangle_it 2.687 r_scbond_it 1.507 r_angle_refined_deg 1.407 r_mcangle_it 1.189 r_mcbond_it 0.622 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.104 r_dihedral_angle_4_deg 22.26 r_dihedral_angle_3_deg 19.83 r_dihedral_angle_1_deg 6.219 r_scangle_it 2.687 r_scbond_it 1.507 r_angle_refined_deg 1.407 r_mcangle_it 1.189 r_mcbond_it 0.622 r_nbtor_refined 0.315 r_symmetry_hbond_refined 0.276 r_nbd_refined 0.232 r_symmetry_vdw_refined 0.186 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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_refined 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6077 Nucleic Acid Atoms 478 Solvent Atoms 1 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing