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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 1-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 7 294 100 mM Hepes pH 7.0, 6% PEG 4000, 5 mM SrCl2
Crystal Properties Matthews coefficient Solvent content 2.67 53.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.995 α = 90 b = 210.414 β = 108.6 c = 47.752 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 2017-04-11 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 3.3 50 99.8 24 4.4 12200
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 3.31 35 11550 620 99.16 0.22617 0.22357 0.2241 0.27857 0.2726 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] 4.63 -1.43 -9.38 4.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.184 r_dihedral_angle_3_deg 15.911 r_dihedral_angle_4_deg 14.783 r_long_range_B_refined 10.271 r_long_range_B_other 10.27 r_mcangle_it 7.375 r_mcangle_other 7.374 r_scangle_other 6.698 r_dihedral_angle_1_deg 5.855 r_mcbond_other 4.422
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.184 r_dihedral_angle_3_deg 15.911 r_dihedral_angle_4_deg 14.783 r_long_range_B_refined 10.271 r_long_range_B_other 10.27 r_mcangle_it 7.375 r_mcangle_other 7.374 r_scangle_other 6.698 r_dihedral_angle_1_deg 5.855 r_mcbond_other 4.422 r_mcbond_it 4.421 r_scbond_it 3.858 r_scbond_other 3.855 r_angle_refined_deg 1.111 r_angle_other_deg 0.913 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 78 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing