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Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal Contacts
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 4.5 277 40% MPD, 1MM CUPRIC ACETATE, 10MM SODIUM ACETATE, pH 4.50, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.58 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.209 α = 90 b = 49.557 β = 113.33 c = 59.427 γ = 90
Symmetry Space Group C 1 2 1
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 210 MIRROR 2005-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A Photon Factory AR-NW12A
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 1.9 54.55 99.5 0.083 0.083 3.7 18923 18812
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 1.9 1.97 99.9 0.304 0.304 3.7
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 2TRX 1.9 41.6 16882 1930 99.47 0.18731 0.18374 0.1875 0.21845 0.2222 RANDOM 18.98
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] -0.35 -0.29 1.05 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.951 r_dihedral_angle_3_deg 12.627 r_dihedral_angle_4_deg 11.566 r_dihedral_angle_1_deg 4.951 r_scangle_it 4.59 r_scbond_it 2.98 r_mcangle_it 1.884 r_angle_refined_deg 1.584 r_mcbond_it 1.233 r_symmetry_vdw_refined 0.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.951 r_dihedral_angle_3_deg 12.627 r_dihedral_angle_4_deg 11.566 r_dihedral_angle_1_deg 4.951 r_scangle_it 4.59 r_scbond_it 2.98 r_mcangle_it 1.884 r_angle_refined_deg 1.584 r_mcbond_it 1.233 r_symmetry_vdw_refined 0.394 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.275 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.111 r_metal_ion_refined 0.039 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1627 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 18
Software Software Software Name Purpose MOLREP phasing CNS refinement HKL-2000 data reduction SCALEPACK data scaling REFMAC refinement