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Crystal structure of ribonucleotide reductase NrdF from Bacillus anthracis anaerobically soaked with ferrous ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QO5
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 2.19 43.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.558 α = 90 b = 61.456 β = 106.589 c = 95.794 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 6M 2014-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.319 45.903 97.86 0.04 0.048 0.026 0.999 14.7 3.2 147577 12.7813381668
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.319 1.37 87.89 0.437 0.559 0.343 0.817 1.75 2.3
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 6QO5 1.31921770161 45.9034025688 1.35846052973 147259 7360 97.8315606253 0.135057759383 0.133724482784 0.1363 0.160607752928 0.1625 Random selection 19.2211682502
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 21.4003567822 f_angle_d 1.13518638725 f_chiral_restr 0.0783704317059 f_bond_d 0.010804611391 f_plane_restr 0.0076840154793
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4648 Nucleic Acid Atoms Solvent Atoms 546 Heterogen Atoms 43
Software Software Software Name Purpose XDS data reduction PHASER phasing SCALA data scaling PHENIX refinement