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Crystal structure of the anaerobic ribonucleotide reductase from Thermotoga maritima with dATP bound in the specificity site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4COI PDB ENTRY 4COI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 A NATIVE CRYSTAL (20 MG/ML, 12% [W/V] PEG3000, 100 MM MES PH 5.9, 5 MM DTT) SOAKED WITH 0.5 MM DATP, 10 MM MGCL2 AND 20% (V/V) PEG400
Crystal Properties Matthews coefficient Solvent content 1.95 37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78 α = 90 b = 94.12 β = 112.03 c = 86.71 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 225 mm CCD TOROIDAL MIRROR FOR HORIZONTAL AND VERTICAL FOCUSING 2013-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 MAX II I911-3
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 1.96 29.1 99.1 0.08 14.8 4.3 82717 24.92
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 1.96 2.08 98.7 0.63 2.1 4.2
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 4COI 1.96 29.136 1.35 82656 2078 99.23 0.192 0.1911 0.2255 0.205
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 14.796 f_angle_d 1.027 f_chiral_restr 0.061 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9639 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 72
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling REFMAC phasing