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Crystal Structure of M. tuberculosis Thioredoxin reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TDE PDB entry 1TDE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 15% PEG 3350, Sodium phosphate citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 51.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.4 α = 90 b = 107.4 β = 90 c = 118.2 γ = 90
Symmetry Space Group P 41 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 CCD MARRESEARCH 2003-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 0.927 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 3 50 97 0.081 0.083 16.2 2.2 14186 89
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 97.9 0.369 0.345 14.8 2.1 1368
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 PDB entry 1TDE 3 36 13357 707 97.89 0.21508 0.21132 0.2181 0.29066 0.3031 RANDOM 59.802
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] 0.29 0.29 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.921 r_dihedral_angle_3_deg 19.761 r_dihedral_angle_4_deg 18.114 r_scangle_it 13.589 r_scbond_it 10.176 r_dihedral_angle_1_deg 6.21 r_mcangle_it 4.221 r_mcbond_it 2.863 r_angle_refined_deg 1.346 r_angle_other_deg 1.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.921 r_dihedral_angle_3_deg 19.761 r_dihedral_angle_4_deg 18.114 r_scangle_it 13.589 r_scbond_it 10.176 r_dihedral_angle_1_deg 6.21 r_mcangle_it 4.221 r_mcbond_it 2.863 r_angle_refined_deg 1.346 r_angle_other_deg 1.013 r_mcbond_other 0.557 r_metal_ion_refined 0.347 r_symmetry_vdw_other 0.23 r_nbd_refined 0.228 r_nbd_other 0.206 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.174 r_symmetry_hbond_refined 0.166 r_symmetry_vdw_refined 0.163 r_nbtor_other 0.085 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4592 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 204
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing