☰ Navigation Tabs
Crystal structure of a dA:O-allylhydroxylamine-dC basepair in complex with fragment DNA polymerase I from Bacillus stearothermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U45 PDB ENTRY 1U45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.8 50-55% (NH4)2SO4 3-3.5% MPD 100MM MES, PH 5.8 10MG/ML PROTEIN/DNA 1:3
Crystal Properties Matthews coefficient Solvent content 3.26 66.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.478 α = 90 b = 93.636 β = 90 c = 105.091 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 MARRESEARCH 2009-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
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 2.85 43.74 99.7 0.083 13.3 3.6 20704 2
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 2.85 3 100 0.399 3.3 3.7
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 1U45 2.85 43.74 19570 1047 99.4 0.216 0.215 0.2141 0.245 0.2506 RANDOM 33.17
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] 4.92 -3.45 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.473 r_dihedral_angle_4_deg 18.326 r_dihedral_angle_3_deg 18.074 r_dihedral_angle_1_deg 4.878 r_scangle_it 2.917 r_scbond_it 1.675 r_angle_refined_deg 1.384 r_mcangle_it 0.967 r_angle_other_deg 0.887 r_mcbond_it 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.473 r_dihedral_angle_4_deg 18.326 r_dihedral_angle_3_deg 18.074 r_dihedral_angle_1_deg 4.878 r_scangle_it 2.917 r_scbond_it 1.675 r_angle_refined_deg 1.384 r_mcangle_it 0.967 r_angle_other_deg 0.887 r_mcbond_it 0.47 r_mcbond_other 0.089 r_chiral_restr 0.069 r_bond_refined_d 0.013 r_bond_other_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.001 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_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 4633 Nucleic Acid Atoms 428 Solvent Atoms 7 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing