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Crystal structure of a salicylic aldehyde base in the pre-insertion site of 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 Crystal Properties Matthews coefficient Solvent content 3.27 62.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.037 α = 90 b = 94.022 β = 90 c = 106.711 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 PIXEL DECTRIS PILATUS 6M 2010-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 3.05 46.4 99 0.15 9.5 3.4 16829 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 3.05 3.21 99.1 0.53 3 3.5
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 3.05 43.02 15959 836 98.54 0.23853 0.23618 0.2413 0.28373 0.2885 RANDOM 30.531
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] 7.43 -3.36 -4.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.644 r_dihedral_angle_4_deg 19.342 r_dihedral_angle_3_deg 19.25 r_dihedral_angle_1_deg 4.833 r_angle_other_deg 4.121 r_scangle_it 2.277 r_scbond_it 1.223 r_angle_refined_deg 1.121 r_mcangle_it 0.409 r_mcbond_it 0.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.644 r_dihedral_angle_4_deg 19.342 r_dihedral_angle_3_deg 19.25 r_dihedral_angle_1_deg 4.833 r_angle_other_deg 4.121 r_scangle_it 2.277 r_scbond_it 1.223 r_angle_refined_deg 1.121 r_mcangle_it 0.409 r_mcbond_it 0.197 r_chiral_restr 0.055 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d 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_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 4497 Nucleic Acid Atoms 423 Solvent Atoms 8 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing