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Structure of the reduced 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. SOACKING IN A TRISHYDROXIMETHYLPHOSPHINE SOLUTION 10MM
Crystal Properties Matthews coefficient Solvent content 2.6 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.58 α = 87.77 b = 49.61 β = 82.3 c = 80.02 γ = 79.31
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 BENT MIRROR 2004-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A EMBL/DESY, HAMBURG BW7A
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 2 19.4 97.1 0.07 11.42 2.68 50114
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 2 2.1 97.8 0.24 4.29 2.53
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 2 19.23 46290 2442 97.2 0.22 0.217 0.2334 0.284 0.268 RANDOM 15.23
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] -0.16 0.15 0.16 0.11 -0.11 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.744 r_dihedral_angle_3_deg 18.749 r_dihedral_angle_4_deg 18.161 r_scangle_it 8.338 r_dihedral_angle_1_deg 8.109 r_scbond_it 6.445 r_mcangle_it 4.034 r_mcbond_it 3.086 r_angle_refined_deg 2.324 r_nbtor_refined 0.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.744 r_dihedral_angle_3_deg 18.749 r_dihedral_angle_4_deg 18.161 r_scangle_it 8.338 r_dihedral_angle_1_deg 8.109 r_scbond_it 6.445 r_mcangle_it 4.034 r_mcbond_it 3.086 r_angle_refined_deg 2.324 r_nbtor_refined 0.283 r_symmetry_hbond_refined 0.257 r_xyhbond_nbd_refined 0.217 r_chiral_restr 0.155 r_nbd_refined 0.059 r_symmetry_vdw_refined 0.037 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 498 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling