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structure of the oxidised form of human thioredoxin 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UVZ PDB ENTRY 1UVZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 PEG 3350 22% (W/V) NA ACETATE 0.1M (PH 4.6) AMMONIUM SULFATE 0.2M DTT 1MM. SOAKING IN A H2O2 SOLUTION 1MM
Crystal Properties Matthews coefficient Solvent content 2.3 45.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.06 α = 87.75 b = 49.14 β = 82.77 c = 78.71 γ = 79.2
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 M1 AND M2 MIRRORS 2003-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 20 99.3 0.06 11.67 2.22 65984
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 99.9 0.27 3.4 2.45
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 1UVZ 1.8 19.32 62615 3368 99.4 0.172 0.169 0.2137 0.228 0.2391 RANDOM 11.32
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] -0.03 0.02 -0.08 -0.04 -0.07 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.919 r_scangle_it 5.925 r_scbond_it 4.456 r_angle_refined_deg 2.947 r_mcangle_it 2.665 r_mcbond_it 2.108 r_angle_other_deg 1.373 r_symmetry_vdw_other 0.326 r_nbd_other 0.276 r_nbd_refined 0.231
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.919 r_scangle_it 5.925 r_scbond_it 4.456 r_angle_refined_deg 2.947 r_mcangle_it 2.665 r_mcbond_it 2.108 r_angle_other_deg 1.373 r_symmetry_vdw_other 0.326 r_nbd_other 0.276 r_nbd_refined 0.231 r_symmetry_vdw_refined 0.215 r_chiral_restr 0.212 r_xyhbond_nbd_refined 0.193 r_symmetry_hbond_refined 0.183 r_nbtor_other 0.097 r_gen_planes_other 0.018 r_gen_planes_refined 0.014 r_bond_refined_d 0.012 r_bond_other_d 0.01 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined 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 r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5074 Nucleic Acid Atoms Solvent Atoms 763 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling