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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 3BK1 PDB ENTRY 3BK1
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.
Crystal Properties Matthews coefficient Solvent content 4.9 0.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.187 α = 90 b = 186.187 β = 90 c = 113.382 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 6M 2012-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 2.28 35 99.3 0.05 10.6 8.2 88741 3
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 2.28 2.3 97.9 0.49 2.5 7.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD PDB ENTRY 3BK1 2.283 29.34 1.21 88509 8404 96.99 0.1463 0.1446 0.1498 0.1769 0.1811
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 13.812 f_angle_d 1.206 f_chiral_restr 0.051 f_bond_d 0.009 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6950 Nucleic Acid Atoms 216 Solvent Atoms 558 Heterogen Atoms 18
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling SHELX phasing PHENIX phasing PHENIX refinement