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Crystal structure of the RNA polymerase domain (RPD) of Mycobacterium tuberculosis primase DnaG in complex with a double-stranded DNA oligomer with a 6-nucleotide overhang
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5W34
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 100 mM sodium citrate pH 6.0, 5% w/v PEG 4000 and 5 mM SrCl2
Crystal Properties Matthews coefficient Solvent content 2.72 54.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.837 α = 90 b = 210.936 β = 106.78 c = 46.046 γ = 90
Symmetry Space Group P 1 21 1
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 RAYONIX MX300-HS 2017-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 2.45 50 96.2 23 2.7 27849
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 5W34 2.46 35 26558 1253 95.72 0.21775 0.21513 0.2162 0.26915 0.2618 RANDOM
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] 3.01 -1.2 -2.8 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.116 r_dihedral_angle_3_deg 17.301 r_dihedral_angle_4_deg 16.644 r_long_range_B_refined 7.578 r_long_range_B_other 7.578 r_dihedral_angle_1_deg 6.157 r_scangle_other 5.232 r_mcangle_it 4.907 r_mcangle_other 4.906 r_scbond_it 3.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.116 r_dihedral_angle_3_deg 17.301 r_dihedral_angle_4_deg 16.644 r_long_range_B_refined 7.578 r_long_range_B_other 7.578 r_dihedral_angle_1_deg 6.157 r_scangle_other 5.232 r_mcangle_it 4.907 r_mcangle_other 4.906 r_scbond_it 3.359 r_scbond_other 3.357 r_mcbond_it 3.021 r_mcbond_other 3.021 r_angle_refined_deg 1.259 r_angle_other_deg 0.954 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4932 Nucleic Acid Atoms 42 Solvent Atoms 47 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing