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Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 2.1-2.5M ammonium sulfate, 0.1M MES or HEPES, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.3 46.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.152 α = 90.1 b = 49.193 β = 103.2 c = 88.039 γ = 90.01
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 173 CCD ADSC QUANTUM 210 2009-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 1.8 50 95.5 0.054 15.9 2 57629
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) 1.8 1.86 85.2 0.229 2.2 1.8 5146
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 30 54693 2930 94.77 0.19843 0.19573 0.1945 0.25028 0.2477 RANDOM 23.602
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] 1.23 -0.07 -0.28 -0.3 -0.3 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.592 r_dihedral_angle_4_deg 16.239 r_dihedral_angle_3_deg 13.263 r_dihedral_angle_1_deg 5.839 r_scangle_it 3.667 r_scbond_it 2.406 r_mcangle_it 1.421 r_angle_refined_deg 1.334 r_mcbond_it 0.852 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.592 r_dihedral_angle_4_deg 16.239 r_dihedral_angle_3_deg 13.263 r_dihedral_angle_1_deg 5.839 r_scangle_it 3.667 r_scbond_it 2.406 r_mcangle_it 1.421 r_angle_refined_deg 1.334 r_mcbond_it 0.852 r_nbtor_refined 0.306 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.167 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4988 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms 40
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling