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Methylmalonyl-CoA decarboxylase in complex with 2-nitronate-propionyl-oxa(dethia)-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6N92
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 150 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 2.79 55.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.179 α = 90 b = 114.653 β = 90 c = 194.554 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 MARMOSAIC 300 mm CCD 2016-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 94 0.109 0.11 0.119 0.047 5.2 6.2 203268 -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 1.73 93.8 1.192 1.192 1.167 5.9
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 6N92 1.7 28.68 177818 9300 86.25 0.1546 0.153 0.1654 0.1839 0.1924 RANDOM 16.898
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] -0.07 -0.3 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.035 r_dihedral_angle_4_deg 16.002 r_dihedral_angle_3_deg 13.792 r_dihedral_angle_1_deg 6.326 r_mcangle_it 2.518 r_angle_refined_deg 1.81 r_mcbond_other 1.595 r_mcbond_it 1.594 r_angle_other_deg 1.478 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.035 r_dihedral_angle_4_deg 16.002 r_dihedral_angle_3_deg 13.792 r_dihedral_angle_1_deg 6.326 r_mcangle_it 2.518 r_angle_refined_deg 1.81 r_mcbond_other 1.595 r_mcbond_it 1.594 r_angle_other_deg 1.478 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12246 Nucleic Acid Atoms Solvent Atoms 2018 Heterogen Atoms 472
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing