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Structure of Rhyzopertha dominica dihydrolipoyl dehydrogenase variant C83A in pre-covalent complex with aspartyl-lipoyllysine at 1.64 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other In-house structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 Tris, magnesium chloride, sodium chloride, PEG3350, formamide
Crystal Properties Matthews coefficient Solvent content 2.18 43.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.916 α = 90 b = 91.77 β = 90 c = 142.955 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 PIXEL DECTRIS EIGER2 X CdTe 16M 2023-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.97625 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.64 77.227 99.1 0.104 0.999 15 4.5 107437 18.05
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.672 99.9 1.139 0.78 2.1 9.2
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 1.64 35.74 1.35 107414 5213 99.88 0.1509 0.1493 0.1502 0.1832 0.183 23.63
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 14.0604 f_angle_d 0.8506 f_chiral_restr 0.0702 f_plane_restr 0.0057 f_bond_d 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7041 Nucleic Acid Atoms Solvent Atoms 1242 Heterogen Atoms 149
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing