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Crystal structure of S. thermophilus class III ribonucleotide reductase bound to dATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H79
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 296.15 Crystals were grown at room temperature in 1.5 M ammonium sulfate, 0.1 M HEPES pH 7.0. Crystals were cryo-protected and nucleotides were introduced by looping through a solution of 15 % glycerol, 1.5 M ammonium sulfate, 100 mM ammonium formate, 30 mM magnesium sulfate, 1 mM TCEP, 50 mM HEPES, 10 mM CTP, 10 mM dATP and plunged directly in liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.51 50.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.58 α = 90 b = 97.885 β = 90 c = 189.202 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 CCD ADSC QUANTUM 315 2014-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.6 48.94 99.83 0.998 15.98 10.2 52393
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.65 98.9 0.925 10.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.6 48.94 1.34 52383 2613 99.83 0.1757 0.1729 0.1744 0.2317 0.2328 47.18
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 12.9359 f_angle_d 0.476 f_chiral_restr 0.0399 f_plane_restr 0.0039 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11170 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 261
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing