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structure of human thioredoxin 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ERT PDB ENTRY 1ERT
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, pH 4.60
Crystal Properties Matthews coefficient Solvent content 2.3 45.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.038 α = 87.96 b = 49.087 β = 83.19 c = 78.977 γ = 79.08
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH BENT MIRROR 2002-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 23.5 96.9 0.06 9.72 2.11 47020
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 2.2 90.4 0.22 4.22 2
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 1ERT 2.01 23.25 44625 2395 98.1 0.203 0.2 0.2051 0.265 0.2658 RANDOM 12.82
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] -1.21 0.86 0.09 -0.15 -1.11 1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.557 r_scangle_it 4.445 r_scbond_it 2.828 r_angle_refined_deg 2.017 r_mcangle_it 1.699 r_angle_other_deg 1.345 r_mcbond_it 0.991 r_xyhbond_nbd_refined 0.247 r_symmetry_hbond_refined 0.239 r_symmetry_vdw_other 0.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.557 r_scangle_it 4.445 r_scbond_it 2.828 r_angle_refined_deg 2.017 r_mcangle_it 1.699 r_angle_other_deg 1.345 r_mcbond_it 0.991 r_xyhbond_nbd_refined 0.247 r_symmetry_hbond_refined 0.239 r_symmetry_vdw_other 0.216 r_nbd_other 0.2 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.163 r_chiral_restr 0.13 r_nbtor_other 0.092 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_gen_planes_other 0.01 r_bond_other_d 0.007 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 525 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling BEAST phasing