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Crystal structure of the R460G disease-causing mutant of the human dihydrolipoamide dehydrogenase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZMD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 293.15 protein in: 100 mM Tris,150 mM NaCl, 1 mM EDTA, pH 8.0
reservoir solution: 2 M (NH4)2SO4, 2 v/v% PEG-400, 0.1 M HEPES (pH 6.9)
volume ratio: 1
Crystal Properties Matthews coefficient Solvent content 2.92 57.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.913 α = 90 b = 169.497 β = 90 c = 61.401 γ = 90
Symmetry Space Group P 21 21 2
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 2017-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.76 48.4 93 0.141 0.998 9.5 6.8 114691
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.86 71.2 0.255 0.365 0.59 6.7
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 1ZMD 1.76 30 111625 2083 92.19 0.1883 0.18737 0.1995 0.2374 0.2513 RANDOM 33.417
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] 0.87 -2.95 2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.678 r_dihedral_angle_3_deg 15.39 r_dihedral_angle_4_deg 11.847 r_long_range_B_refined 7.407 r_long_range_B_other 7.406 r_dihedral_angle_1_deg 6.636 r_scangle_other 5.779 r_scbond_it 3.927 r_scbond_other 3.926 r_mcangle_it 3.457
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.678 r_dihedral_angle_3_deg 15.39 r_dihedral_angle_4_deg 11.847 r_long_range_B_refined 7.407 r_long_range_B_other 7.406 r_dihedral_angle_1_deg 6.636 r_scangle_other 5.779 r_scbond_it 3.927 r_scbond_other 3.926 r_mcangle_it 3.457 r_mcangle_other 3.457 r_mcbond_it 2.632 r_mcbond_other 2.63 r_angle_refined_deg 1.893 r_angle_other_deg 1.036 r_chiral_restr 0.114 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7072 Nucleic Acid Atoms Solvent Atoms 904 Heterogen Atoms 169
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data scaling XDS data reduction MOLREP phasing