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Succinyl-CoA Reductase from Clostridium kluyveri (SucD) with NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8CEI other deposition
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 288.15 45 % w/v Pentaerythritol Propoxylate (5/4 PO/OH)
100 mM MES; pH 6.5
400 mM Potassium chloride
Crystal Properties Matthews coefficient Solvent content 3.23 61.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.046 α = 90 b = 190.828 β = 90 c = 190.907 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 6M 2019-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97620 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 2.04 39.44 98.6 0.215 0.059 0.998 8.5 12.8 159239
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) 2.04 2.15 90.4 2.931 0.966 0.329 8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.15 29.66 1.34 138025 2004 99.9 0.1983 0.198 0.1988 0.2219 0.2214
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 12.407 f_angle_d 0.585 f_chiral_restr 0.047 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13813 Nucleic Acid Atoms Solvent Atoms 1066 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling PHENIX refinement XDS data reduction PHASER phasing