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Crystal structure of the RNA polymerase domain (RPD) of Mycobacterium tuberculosis primase DnaG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DDE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 294 1.85 M ammonium sulfate, 50 mM Tris pH 8.5 and 5% v/v PEG 400, 1 mM MnCl2
Crystal Properties Matthews coefficient Solvent content 4.24 70.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.495 α = 90 b = 117.495 β = 90 c = 87.089 γ = 90
Symmetry Space Group P 4 2 2
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 2015-08-17 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 2.85 50 99.2 18 4.4 14758 1.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1DDE 2.85 35 13944 737 99.12 0.2423 0.2407 0.27294 0.2492 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] 0.56 0.56 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.583 r_dihedral_angle_4_deg 16.585 r_dihedral_angle_3_deg 15.414 r_dihedral_angle_1_deg 5.529 r_long_range_B_refined 4.756 r_long_range_B_other 4.755 r_mcangle_it 2.881 r_mcangle_other 2.88 r_scangle_other 2.208 r_mcbond_it 1.574
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.583 r_dihedral_angle_4_deg 16.585 r_dihedral_angle_3_deg 15.414 r_dihedral_angle_1_deg 5.529 r_long_range_B_refined 4.756 r_long_range_B_other 4.755 r_mcangle_it 2.881 r_mcangle_other 2.88 r_scangle_other 2.208 r_mcbond_it 1.574 r_mcbond_other 1.574 r_scbond_it 1.195 r_scbond_other 1.195 r_angle_refined_deg 1.081 r_angle_other_deg 0.894 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 2357 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing