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Isobutyryl-CoA mutase fused with bound adenosylcobalamin, GDP, Mg (holo-IcmF/GDP), and substrate n-butyryl-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 7.0.
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 n-butyryl-coenzyme A for 30 s
Crystal Properties Matthews coefficient Solvent content 6.7 82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 316.76 α = 90 b = 316.76 β = 90 c = 342.67 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 3.5 35 98.4 0.148 12.7 5.1 81568
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 3.5 3.59 99.2 2 5.1
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 3.5 34.819 81538 4119 98.52 0.1864 0.1853 0.192 0.2088 0.2128 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 10.88 f_angle_d 0.592 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 16169 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 340
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling Coot model building PHENIX phasing