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Crystal structure of an artificial salen-copper 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 Crystal Properties Matthews coefficient Solvent content 3.3 62.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.171 α = 90 b = 93.469 β = 90 c = 105.591 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 2009-12-07 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 2.22 93.47 99.9 0.08 14.9 4.8 43840 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 2.22 2.34 99.9 0.43 3.5 4.8
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 2.22 67.68 41587 2189 100 0.1952 0.19314 0.1934 0.23464 0.2308 RANDOM 21.675
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] 2.2 -1.26 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.037 r_dihedral_angle_4_deg 21.697 r_dihedral_angle_3_deg 14.113 r_dihedral_angle_1_deg 5.434 r_scangle_it 3.316 r_scbond_it 2.063 r_angle_refined_deg 1.469 r_mcangle_it 1.327 r_angle_other_deg 0.904 r_mcbond_it 0.685
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.037 r_dihedral_angle_4_deg 21.697 r_dihedral_angle_3_deg 14.113 r_dihedral_angle_1_deg 5.434 r_scangle_it 3.316 r_scbond_it 2.063 r_angle_refined_deg 1.469 r_mcangle_it 1.327 r_angle_other_deg 0.904 r_mcbond_it 0.685 r_mcbond_other 0.145 r_chiral_restr 0.079 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 4572 Nucleic Acid Atoms 404 Solvent Atoms 183 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing