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Crystal Structure of Mycobacterium smegmatis thioredoxin reductase in complex with Z854627136
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 3 58.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.92 α = 90 b = 67.92 β = 90 c = 155.565 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 PILATUS3 6M 2025-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 1.87 32.44 98.97 0.995 7.88 6.2 35119 32.61
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 1.87 1.937 0.316
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 1.87 32.44 1.33 34856 1718 99.01 0.2108 0.2088 0.2089 0.2506 0.2505 43.66
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 18.3892 f_angle_d 1.0734 f_chiral_restr 0.0623 f_plane_restr 0.0091 f_bond_d 0.0086
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2306 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 109
Software Software Software Name Purpose MxCuBE data collection DIALS data reduction DIALS data scaling PHENIX phasing PHENIX refinement