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Isobutyryl-CoA mutase fused with bound adenosylcobalamin, GDP, Mg (holo-IcmF/GDP), and substrate isovaleryl-coenzyme A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XC6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 precipitant: 700 mM potassium sodium tartrate, 200 mM ammonium acetate, 100 mM imidazole pH 7.7.
3% (v/v) ethylene glycol additive in drop solution only.
protein in 100 mM NaCl, 50 mM HEPES pH 7.5, 1 mM GDP, 3 mM MgCl2, 0.3 mM adenosylcobalamin, mixed with precipitant 1 uL + 1 uL
set up under red light, grown in the dark, soaked with 5 mM isovaleryl-coenzyme A for 30 s
Crystal Properties Matthews coefficient Solvent content 6.7 82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 317.56 α = 90 b = 317.56 β = 90 c = 343.52 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 CCD ADSC QUANTUM 315 2011-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9795 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 3.45 35 99 0.137 10 3.8 86230
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 3.45 3.54 99.9 2 3.8
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 4XC6 3.45 34.906 86185 4353 99.03 0.1938 0.1927 0.1979 0.2144 0.2175 copied from entry 4XC6
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 10.803 f_angle_d 0.595 f_chiral_restr 0.023 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16160 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 341
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling Coot model building