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Methylmalonyl-CoA decarboxylase in complex with 2-sulfonate-propionyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EF8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 200 mM sodium chloride, 100 mM imidazole, 0.4 Monosodium phosphate/1.6 M Dipotassium phosphate, 4% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.76 55.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.927 α = 90 b = 114.421 β = 90 c = 193.43 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX300HE 2017-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.798 30 100 0.165 0.165 0.177 0.065 4.9 7.3 178862 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 100 1.395 1.395 1.4 7.2
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1EF8 1.798 19.997 178638 8931 99.688 0.1593 0.162 0.1922 0.1917 25.421
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] -0.009 0.008 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.232 r_dihedral_angle_4_deg 16.825 r_dihedral_angle_3_deg 14.005 r_lrange_it 6.264 r_lrange_other 6.256 r_dihedral_angle_1_deg 6.23 r_scangle_it 5.097 r_scangle_other 5.096 r_scbond_it 3.381 r_scbond_other 3.381
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.232 r_dihedral_angle_4_deg 16.825 r_dihedral_angle_3_deg 14.005 r_lrange_it 6.264 r_lrange_other 6.256 r_dihedral_angle_1_deg 6.23 r_scangle_it 5.097 r_scangle_other 5.096 r_scbond_it 3.381 r_scbond_other 3.381 r_mcangle_it 2.773 r_mcangle_other 2.773 r_mcbond_it 1.993 r_mcbond_other 1.993 r_angle_refined_deg 1.724 r_angle_other_deg 1.042 r_metal_ion_refined 0.33 r_symmetry_nbd_refined 0.33 r_nbd_other 0.266 r_nbd_refined 0.223 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.138 r_symmetry_xyhbond_nbd_refined 0.125 r_symmetry_nbtor_other 0.076 r_symmetry_xyhbond_nbd_other 0.024 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_symmetry_metal_ion_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12246 Nucleic Acid Atoms Solvent Atoms 1777 Heterogen Atoms 713
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing