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Methylsuccinyl-CoA dehydrogenase from Pseudomonas migulae with bound FAD and (2S)-methylsuccinyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ES9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 Enzyme (20 mg/mL) in 25 mM MOPS pH 7.5 and 0.2 M NaCl was mixed in a 1:1 ratio with crystallization condition (0.2 M ammonium citrate pH 5.0, 20% (w/v) PEG 3350).
Soaking and cryoprotection of crystals was performed by adding methylsuccinyl-CoA and PEG200 to final concentrations of 16 mM and 40% (v/v), respectively, before crystals were plunge frozen in liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.94 58.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.805 α = 90 b = 169.563 β = 90 c = 118.39 γ = 90
Symmetry Space Group C 2 2 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 PILATUS 6M-F 2019-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.93 25.01 99.7 0.124 0.034 0.999 14.6 13.2 105292
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.93 2.03 98.6 1.213 0.337 0.892 12.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.93 25.01 0.97 105172 1997 99.7 0.1744 0.1739 0.2027 0.201
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 15.643 f_angle_d 0.967 f_chiral_restr 0.052 f_bond_d 0.009 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8632 Nucleic Acid Atoms Solvent Atoms 567 Heterogen Atoms 26
Software Software Software Name Purpose SCALA data scaling PHENIX refinement XDS data reduction PHENIX phasing