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Methylmalonyl-CoA decarboxylase in complex with 2-sulfonate-propionyl-oxa(dethia)-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 8 298 100 mM sodium chloride, 100 mM imidazole, 0.4 M Monosodium phosphate/1.6 M Dipotassium phosphate, 2% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.76 55.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.148 α = 90 b = 114.66 β = 90 c = 192.705 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 PIXEL DECTRIS EIGER X 9M 2017-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97849 APS 21-ID-D
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 1.7 30 90.8 0.099 0.105 0.108 0.042 9.7 6.1 191624 -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 1.7 1.76 90.7 0.84 0.84 2.116 5.7
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 THROUGHOUT 1EF8 1.7 29.96 177529 9281 88.16 0.1525 0.1509 0.1633 0.1839 0.1918 RANDOM 15.736
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] -0.1 0.01 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.659 r_dihedral_angle_4_deg 15.938 r_dihedral_angle_3_deg 13.422 r_dihedral_angle_1_deg 6.134 r_mcangle_it 2.296 r_angle_refined_deg 2.009 r_mcbond_it 1.495 r_mcbond_other 1.495 r_angle_other_deg 1.483 r_chiral_restr 0.161
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.659 r_dihedral_angle_4_deg 15.938 r_dihedral_angle_3_deg 13.422 r_dihedral_angle_1_deg 6.134 r_mcangle_it 2.296 r_angle_refined_deg 2.009 r_mcbond_it 1.495 r_mcbond_other 1.495 r_angle_other_deg 1.483 r_chiral_restr 0.161 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 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 1882 Heterogen Atoms 739
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing