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Thermotoga maritima Ribonucleotide Reductase, NrdJ, in complex with dTTP, GDP and Adenosylcobalamin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XJE PDB entry 1XJE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 10% PEG8000, 0.1M sodium acetate, 0.1 M sodium chloride, 10mM DTT (dithiotreithol), 5% glycerol, crystallization geometry: 4 microL protein 11miligram/milliL + 2uL reservoir solution over 300 microL in 24-well plate. Crystals in 3-4 days, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.66 53.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.02 α = 90 b = 124.23 β = 102.57 c = 107.17 γ = 90
Symmetry Space Group C 1 2 1
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 210 2005-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.979162 ESRF ID29
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 1.9 49 99.4 0.064 4.42 120492 119789 31.5
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 1.9 2 99.6 0.848 1.6 3.75 17143
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 Rigid body refinement PDB entry 1XJE 1.9 46.937 1.35 120492 119774 5993 99.45 0.204 0.2022 0.2009 0.2378 0.2371
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] 10.6805 8.1781 -1.9529 -8.7276
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.843 f_angle_d 1.139 f_chiral_restr 0.073 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9874 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms 334
Software Software Software Name Purpose PHENIX refinement REFMAC refinement ProDC data collection XDS data reduction XSCALE data scaling REFMAC phasing