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Crystal structure of the oxidised form of thioredoxin 1 from saccharomyces cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FA4 PDB ENTRY 2FA4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 291 4% PEG400, 12%PEG8000, 0.1M sodium acetate, 0.2M zinc acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2 38.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.292 α = 90 b = 46.588 β = 90 c = 64.2 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 IMAGE PLATE RIGAKU RAXIS IV 2006-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 1.7 37.706 97.4 0.041 11.9 10873 2 2 23.07
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) 1.76 1.83 96.4 0.04 2.7 1044
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2FA4 1.76 28.85 2 9938 9472 466 98.57 0.2 0.1999 0.19758 0.2019 0.24547 0.2525 RANDOM 26.253
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] 1.74 -1.4 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.528 r_dihedral_angle_3_deg 13.58 r_dihedral_angle_1_deg 5.398 r_scangle_it 3.378 r_scbond_it 2.287 r_mcangle_it 1.731 r_angle_refined_deg 1.551 r_mcbond_it 1.087 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.275
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.528 r_dihedral_angle_3_deg 13.58 r_dihedral_angle_1_deg 5.398 r_scangle_it 3.378 r_scbond_it 2.287 r_mcangle_it 1.731 r_angle_refined_deg 1.551 r_mcbond_it 1.087 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.275 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.156 r_symmetry_metal_ion_refined 0.148 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.103 r_metal_ion_refined 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_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_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 848 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 3
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement d*TREK data reduction d*TREK data scaling