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Crystal structure of thioredoxin from the acidophile Acetobacter aceti
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TRX PDB entry 2trx
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 microseeding in 100 mM sodium acetate (pH 4.6), 100 mM ammonium acetate, 24% (w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.97 37.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.94 α = 90 b = 42.24 β = 90 c = 63.67 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 CCD NOIR-1 2006-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.07 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1 42.24 96.2 0.048 23.9 6.13 48392 7.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.04 67.9 0.479 1.8 2.8 3351
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 (All) 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 2trx 1 35.2 45895 2428 96.22 0.13465 0.13465 0.13346 0.1433 0.1582 0.1639 RANDOM 12.51
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] -0.14 0.17 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.081 r_dihedral_angle_4_deg 28.105 r_sphericity_free 15.363 r_dihedral_angle_3_deg 11.38 r_scangle_it 6.804 r_dihedral_angle_1_deg 5.745 r_sphericity_bonded 5.443 r_scbond_it 4.973 r_mcangle_it 3.374 r_mcbond_it 2.711
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.081 r_dihedral_angle_4_deg 28.105 r_sphericity_free 15.363 r_dihedral_angle_3_deg 11.38 r_scangle_it 6.804 r_dihedral_angle_1_deg 5.745 r_sphericity_bonded 5.443 r_scbond_it 4.973 r_mcangle_it 3.374 r_mcbond_it 2.711 r_rigid_bond_restr 2.307 r_angle_refined_deg 2.192 r_angle_other_deg 1.007 r_mcbond_other 0.965 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.223 r_symmetry_vdw_other 0.21 r_nbd_other 0.195 r_nbtor_refined 0.18 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.146 r_nbtor_other 0.098 r_bond_refined_d 0.034 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1684 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement JBluIce-EPICS data collection d*TREK data reduction d*TREK data scaling MOLREP phasing