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Crystal Structure of Mycobacterium smegmatis thioredoxin reductase in complex with Z1280094148
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 59.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.16 α = 90 b = 68.16 β = 90 c = 154.95 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 1.91 46.95 99.9 0.995 8.99 6.6 33162 25.82
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 1.91 1.978 0.337
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 1.91 46.95 1.35 33154 1642 99.92 0.2044 0.2021 0.202 0.2501 0.2507 35.41
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 12.7114 f_angle_d 1.026 f_chiral_restr 0.06 f_plane_restr 0.0094 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2306 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 100
Software Software Software Name Purpose MxCuBE data collection XDS data reduction XDS data scaling PHENIX phasing PHENIX refinement