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Crystal structure of ribonucleotide reductase NrdF from Bacillus anthracis aerobically 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 2.14 42.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.178 α = 90 b = 60.3 β = 106.469 c = 95.831 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 EIGER X 16M 2015-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.04 SLS X06SA
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 1.35 54.3536195985 96.05 0.036 0.049 0.032 0.965 12.3 3.5 131966 13.6832569535
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 1.35 1.39 0.589 0.803 0.548 0.629
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 1.35000968892 54.3536195985 1.97180886301 131718 6665 96.0491774589 0.147741493981 0.146570980629 0.1483 0.168876487598 0.1702 Random selection 22.1813998233
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 24.115268022 f_angle_d 1.09360542879 f_chiral_restr 0.0755164168085 f_bond_d 0.010130872174 f_plane_restr 0.00767919786451
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4625 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing