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Methylmalonyl-CoA decarboxylase in complex with 2-nitronate-propionyl-amino(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 50 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 2.77 55.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.046 α = 90 b = 114.816 β = 90 c = 193.732 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 1.75 30 100 0.125 0.125 0.135 0.05 5.2 7.3 1422149 194971 -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 1.75 1.78 100 1.489 1.489 1.312 7.3
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 1.75 29.29 175192 9164 94.03 0.1473 0.1457 0.1581 0.1777 0.188 RANDOM 21.86
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] -0.32 -0.15 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.653 r_dihedral_angle_4_deg 16.145 r_dihedral_angle_3_deg 14.169 r_dihedral_angle_1_deg 6.36 r_mcangle_it 2.719 r_angle_refined_deg 1.868 r_mcbond_other 1.851 r_mcbond_it 1.85 r_angle_other_deg 1.509 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.653 r_dihedral_angle_4_deg 16.145 r_dihedral_angle_3_deg 14.169 r_dihedral_angle_1_deg 6.36 r_mcangle_it 2.719 r_angle_refined_deg 1.868 r_mcbond_other 1.851 r_mcbond_it 1.85 r_angle_other_deg 1.509 r_chiral_restr 0.116 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 1893 Heterogen Atoms 550
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing