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Succinyl-CoA Reductase from Clostridium kluyveri (SucD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K9D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 288.15 25 % w/v Pentaerythritol Propoxylate (5/4 PO/OH)
100 mM MES; pH 6.5
50 mM Magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.61 52.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.231 α = 90 b = 89.339 β = 104.64 c = 137.322 γ = 90
Symmetry Space Group P 1 21 1
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 2.2 39.47 99.2 0.116 0.054 0.995 7.3 4.4 197254
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) 2.2 2.32 96 0.468 0.22 0.945 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3K9D 2.2 39.47 1.41 197254 3860 97.5 0.2429 0.2424 0.267 0.2788
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 9.886 f_angle_d 0.392 f_chiral_restr 0.042 f_plane_restr 0.003 f_bond_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13576 Nucleic Acid Atoms Solvent Atoms 1024 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHENIX phasing