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Isobutyryl-CoA mutase fused with bound butyryl-CoA, GDP, and Mg and without cobalamin (apo-IcmF/GDP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XC7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 precipitant: 700 - 750 mM sodium potassium tartrate, 100 mM tris pH 8.5
protein in 50 mM NaCl, 20 mM HEPES pH 8, 10 mM butyryl-CoA, mixed with precipitant 1 uL + 1uL
crystal soaked with 1 mM GDP and 1.5 mM MgCl2 for 6 hours
Crystal Properties Matthews coefficient Solvent content 6.7 82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 316.51 α = 90 b = 316.51 β = 90 c = 342.27 γ = 120
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-F 2014-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.25 100 99.3 0.146 11.3 5.1 102338
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.25 3.33 99.6 1.9 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4XC7 3.25 99.159 102263 5143 99.26 0.2063 0.2054 0.2091 0.2218 0.2236 retained from related apo-IcmF set
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 11.235 f_angle_d 0.582 f_chiral_restr 0.021 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16093 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 152
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building