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Crystal structure of thioredoxin from Trypanosoma brucei brucei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ERT Pdb entry 1ert polyala
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 2M sodium formate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.94 36.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.878 α = 90 b = 51.725 β = 90 c = 57.389 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 ADSC QUANTUM 4 2001-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9150 ESRF ID29
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 1.4 30 99.6 0.078 0.078 5.8 10 22807 22807
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 1.4 1.45 100 0.515 0.01 1 10.4 23274
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Pdb entry 1ert polyala 1.4 30 21601 21601 1165 99.68 0.16827 0.1691 0.16762 0.1699 0.19841 RANDOM 14.589
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] 0.57 -0.36 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.511 r_scangle_it 4.229 r_scbond_it 2.478 r_mcangle_it 1.67 r_angle_refined_deg 1.327 r_mcbond_it 0.88 r_angle_other_deg 0.763 r_nbd_refined 0.283 r_symmetry_vdw_other 0.26 r_nbd_other 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.511 r_scangle_it 4.229 r_scbond_it 2.478 r_mcangle_it 1.67 r_angle_refined_deg 1.327 r_mcbond_it 0.88 r_angle_other_deg 0.763 r_nbd_refined 0.283 r_symmetry_vdw_other 0.26 r_nbd_other 0.25 r_xyhbond_nbd_refined 0.187 r_symmetry_vdw_refined 0.168 r_symmetry_hbond_refined 0.137 r_chiral_restr 0.083 r_nbtor_other 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 904 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms
Software Software Software Name Purpose d*TREK data scaling d*TREK data reduction AMoRE phasing REFMAC refinement