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Catalysis and 5' end sensing by ribonuclease RNase J of the metallo- beta-lactamase family
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A0T PDB ENTRY 5A0T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 THE BEST CRYSTALS OF S. COELICOLOR RNASE J WERE OBTAINED IN THE 27.5% W/V PEG 400, 0.1 M TRIS-HCL, PH 8.5 BY MIXING A 1:2 VOLUME RATIO OF CRYSTALLIZATION RESERVOIR TO PROTEIN SOLUTION, THEN SOAKED WITH MNCL2
Crystal Properties Matthews coefficient Solvent content 4.9 0.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.13 α = 90 b = 184.13 β = 90 c = 112.68 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS PILATUS 2015-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 2.7 2.75 99.8 0.14 9.7 6.9 47608 2.5 55.49
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 2.7 2.85 99.5 0.77 2.5 14.4
Refinement Statistics Diffraction ID Structure Solution 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 5A0T 2.8 32.719 0.05 39850 4377 99.17 0.1567 0.1542 0.2084 0.2357
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 14.991 f_angle_d 1.178 f_chiral_restr 0.047 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6950 Nucleic Acid Atoms 196 Solvent Atoms 75 Heterogen Atoms 25
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing