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Uracil Recognition in Archaeal DNA Polymerases Captured by X-ray Crystallography. V93Q polymerase variant
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 5.5 1.9M AMMONIUM SULPHATE, 100MM BIS-TRIS, PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.7 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.432 α = 90 b = 104.747 β = 90 c = 154.408 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 CCD DIAMOND AND GE(220) M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 62 100 0.11 15 5.9 29945
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 2.76 100 0.38 4.4 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 2.6 51 28433 1520 100 0.22 0.217 0.2173 0.275 0.2758 RANDOM 32.5
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.145 r_dihedral_angle_4_deg 17.487 r_dihedral_angle_3_deg 17.15 r_dihedral_angle_1_deg 5.731 r_scangle_it 2.115 r_scbond_it 1.243 r_angle_refined_deg 1.118 r_mcangle_it 0.934 r_mcbond_it 0.487 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.145 r_dihedral_angle_4_deg 17.487 r_dihedral_angle_3_deg 17.15 r_dihedral_angle_1_deg 5.731 r_scangle_it 2.115 r_scbond_it 1.243 r_angle_refined_deg 1.118 r_mcangle_it 0.934 r_mcbond_it 0.487 r_nbtor_refined 0.304 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.182 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.08 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_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 6083 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling