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Mycobacterium tuberculosis Rnase J complex with 7nt RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZQ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 0.2 M Magnesium chloride hexahydrate
0.1 M HEPES pH 7.5
25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.6 52.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.06 α = 90 b = 145.38 β = 90 c = 192.1 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS3 6M 2019-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.2 42.88 99.8 0.0405 16.77 2 21660 59.25
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 3.2 3.314 0.156
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3ZQ4 3.2 42.88 1.34 21631 1067 99.86 0.1879 0.1851 0.1883 0.2406 0.2432 63.03
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 23.0009 f_angle_d 1.3432 f_chiral_restr 0.0778 f_plane_restr 0.0122 f_bond_d 0.0107
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8250 Nucleic Acid Atoms 286 Solvent Atoms Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement HKL-3000 data scaling PHENIX phasing HKL-3000 data reduction