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Crystal structure of trimeric frataxin from the yeast saccharomyces cerevisiae, complexed with cobalt
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FQL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 288 1.7 M (NH4)2SO4, 0.2 M Li2SO4, 4 % -butyrolactone, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 5.43 77.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.2 α = 90 b = 121.2 β = 90 c = 121.2 γ = 90
Symmetry Space Group I 21 3
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 2008-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.605 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 3.2 30 99.8 0.046 25.38 4752 1 1
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 3.2 3.28 99.9 0.493 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 (All) 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 THROUGHOUT 2FQL 3.2 28.57 1 4530 4530 484 99.96 0.20883 0.20883 0.20417 0.21 0.2555 0.2301 RANDOM 95.876
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 r_dihedral_angle_2_deg 42.722 r_dihedral_angle_4_deg 34.477 r_dihedral_angle_3_deg 21.915 r_dihedral_angle_1_deg 10.647 r_scangle_it 2.25 r_angle_refined_deg 1.832 r_scbond_it 1.233 r_mcangle_it 0.941 r_mcbond_it 0.485 r_chiral_restr 0.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.722 r_dihedral_angle_4_deg 34.477 r_dihedral_angle_3_deg 21.915 r_dihedral_angle_1_deg 10.647 r_scangle_it 2.25 r_angle_refined_deg 1.832 r_scbond_it 1.233 r_mcangle_it 0.941 r_mcbond_it 0.485 r_chiral_restr 0.138 r_bond_refined_d 0.014 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 876 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 1
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement XDS data reduction XSCALE data scaling