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Structure of Mycobacterium tuberculosis DnaA-DBD in complex with box1 DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 20 mM Tris, 2 mM MgCl2, 50 mM NaCl, 1200 mM NH4SO4, 2-5% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.04 59.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.441 α = 90 b = 88.441 β = 90 c = 105.156 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD MARMOSAIC 300 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0000 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 50 76.7 52736 40448 3
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 1.7 1.76 26 0.429
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 35 30988 29808 1615 96.19 0.25242 0.25145 0.2579 0.27073 0.2769 RANDOM 41.656
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] 2.71 1.35 2.71 -4.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.71 r_sphericity_bonded 15.772 r_dihedral_angle_3_deg 14.619 r_dihedral_angle_4_deg 12.804 r_scangle_it 7.721 r_scbond_it 4.904 r_rigid_bond_restr 4.851 r_dihedral_angle_1_deg 3.689 r_mcangle_it 3.519 r_mcbond_it 1.797
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.71 r_sphericity_bonded 15.772 r_dihedral_angle_3_deg 14.619 r_dihedral_angle_4_deg 12.804 r_scangle_it 7.721 r_scbond_it 4.904 r_rigid_bond_restr 4.851 r_dihedral_angle_1_deg 3.689 r_mcangle_it 3.519 r_mcbond_it 1.797 r_angle_refined_deg 0.928 r_chiral_restr 0.05 r_sphericity_free 0.013 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1511 Nucleic Acid Atoms 1054 Solvent Atoms 179 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling