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Putative ATP-dependent DNA ligase from Aquifex aeolicus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VUG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.68 54.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.366 α = 90 b = 99.165 β = 90 c = 103.278 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 SBC-2 2003-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-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 2.35 49.6 99.5 0.075 8.7 6.7 39490 39490
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) 2.35 2.39 94.4 0.446 2.05 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2vug 2.35 49.58 39324 37342 1982 98.99 0.20339 0.20062 0.2035 0.25513 0.2646 RANDOM 42.406
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] -2.54 -0.43 2.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.722 r_dihedral_angle_4_deg 21.055 r_dihedral_angle_3_deg 19.782 r_dihedral_angle_1_deg 6.747 r_scangle_it 3.835 r_scbond_it 2.371 r_angle_refined_deg 1.701 r_mcangle_it 1.541 r_angle_other_deg 0.927 r_mcbond_it 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.722 r_dihedral_angle_4_deg 21.055 r_dihedral_angle_3_deg 19.782 r_dihedral_angle_1_deg 6.747 r_scangle_it 3.835 r_scbond_it 2.371 r_angle_refined_deg 1.701 r_mcangle_it 1.541 r_angle_other_deg 0.927 r_mcbond_it 0.81 r_mcbond_other 0.173 r_chiral_restr 0.098 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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_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 127 Heterogen Atoms 52
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing