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Crystal Structure of Mycobacterium smegmatis thioredoxin reductase in complex with Z166687084
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8CCI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 2.16 M Sodium malonate dibasic monohydrate, 10% glycerol , soaked with 5% DMSO
Crystal Properties Matthews coefficient Solvent content 2.97 58.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.77 α = 90 b = 67.77 β = 90 c = 155.13 γ = 120
Symmetry Space Group P 31 2 1
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 2M 2024-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 46.8 99.91 0.997 7.13 6.6 41788 26.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.823 0.527
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 1.76 46.8 1.34 41775 2043 99.92 0.2096 0.2084 0.2085 0.2336 0.2338 35.73
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 13.7742 f_angle_d 1.0593 f_chiral_restr 0.0605 f_plane_restr 0.0094 f_bond_d 0.0081
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2306 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 93
Software Software Software Name Purpose MxCuBE data collection XDS data reduction XDS data scaling PHENIX phasing PHENIX refinement