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Crystal structure of ribonucleotide reductase NrdF L61G variant from Bacillus anthracis anaerobically soaked with Fe(II) and Mn(II) ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QO9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 1.8 - 2.0 M ammonium sulphate, 0.1 M Bis-Tris methane, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.15 42.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.247 α = 90 b = 60.495 β = 106.525 c = 95.996 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 PIXEL DECTRIS PILATUS 2M 2018-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.92 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.76901830909 46.015 98.2 0.054 0.063 0.999 13.97 3.82 60567 22.7525053055
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.88 96.7 0.432 0.507 0.911 2.68 3.625
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6QO9 1.77 41.5580982367 1.35799330492 60442 3018 98.0723673536 0.170746993713 0.168786321429 0.1705 0.208969934425 0.2091 Random selection 30.6597643133
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 15.4556345265 f_angle_d 0.944515286868 f_chiral_restr 0.0485195187157 f_bond_d 0.00820023138162 f_plane_restr 0.00576330187074
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4635 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing