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RNA ligase RtcB from Pyrococcus horikoshii in complex with Co2+ and GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ISZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 apoenzyme: 0.12 mM protein, 2.1 M ammonium sulfate, 0.2 M lithium sulfate
soak: 2.1 M ammonium sulfate, 0.2 M lithium sulfate, 10 mM CoCl2, 10 mM GTP
soak duration: 60 min
cryoprotectant: 2.0 M ammonium sulfate, 0.2 M lithium sulfate, 5 mM CoCl2, 5 mM GTP, 20 % (w/v) sucrose
Crystal Properties Matthews coefficient Solvent content 3.79 67.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.161 α = 90 b = 138.864 β = 90 c = 149.877 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 X 16M 2021-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.6060 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 2.43 49.96 100 0.047 0.995 22.7 19.3 64578 64.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.43 2.49 100 0.337 0.745 2.1 19.4
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 4ISZ 2.43 49.77 1.35 64500 5903 99.99 0.1781 0.1769 0.1833 0.2032 0.2072 77.53
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 13.3416 f_angle_d 1.0363 f_chiral_restr 0.0575 f_plane_restr 0.0089 f_bond_d 0.0078
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7531 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 180
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing