☰ Navigation Tabs
Crystal structure of the RNA polymerase domain (RPD) of Mycobacterium tuberculosis primase DnaG in complex with double-stranded DNA GACCGGAAGTGG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5W33
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 100 mM Hepes pH 7.0, 7% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.84 56.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.781 α = 90 b = 212.116 β = 107.87 c = 47.418 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 2016-07-20 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 2.95 50 94.6 21 4.1 16383 2
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 5W33 2.95 35 15508 781 94.41 0.23829 0.23578 0.2357 0.28532 0.285 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] 5.86 -1.46 -4.12 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.552 r_dihedral_angle_3_deg 17.399 r_dihedral_angle_4_deg 14.224 r_long_range_B_refined 7.21 r_long_range_B_other 7.21 r_dihedral_angle_1_deg 6.081 r_mcangle_it 4.776 r_mcangle_other 4.776 r_scangle_other 4.17 r_mcbond_other 2.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.552 r_dihedral_angle_3_deg 17.399 r_dihedral_angle_4_deg 14.224 r_long_range_B_refined 7.21 r_long_range_B_other 7.21 r_dihedral_angle_1_deg 6.081 r_mcangle_it 4.776 r_mcangle_other 4.776 r_scangle_other 4.17 r_mcbond_other 2.751 r_mcbond_it 2.75 r_scbond_other 2.336 r_scbond_it 2.335 r_angle_refined_deg 1.13 r_angle_other_deg 0.944 r_chiral_restr 0.06 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 4885 Nucleic Acid Atoms 252 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing