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Crystal Structure of Thioredoxin Mutant D10E in Hexagonal (p61) Space Group
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 COUNTER-DIFFUSION 3.5 277 60% (v/v) MPD, HEPES 15 mM pH 4.1, Ac2Cu 1mM, AcNa 15m, pH 3.5, Counter-diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.64 53.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.17 α = 90 b = 103.17 β = 90 c = 41.834 γ = 120
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 BRUKER SMART 6000 Montel Optics 2006-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.25 51.58 99.9 0.0241 27.13 28.93 12308 12308 37.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.3 100 0.1501 6.46 22.28 779
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2TRX 2.25 51.58 12308 12106 1186 98.447 0.202 0.202 0.1954 0.1913 0.268 0.2582 Random 26.62
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] -2.082 -1.041 -2.082 3.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.268 r_dihedral_angle_4_deg 24.691 r_dihedral_angle_3_deg 15.798 r_dihedral_angle_1_deg 5.783 r_mcangle_it 1.832 r_scangle_it 1.648 r_angle_refined_deg 1.403 r_mcbond_it 1.232 r_scbond_it 1.134 r_xyhbond_nbd_refined 0.397
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.268 r_dihedral_angle_4_deg 24.691 r_dihedral_angle_3_deg 15.798 r_dihedral_angle_1_deg 5.783 r_mcangle_it 1.832 r_scangle_it 1.648 r_angle_refined_deg 1.403 r_mcbond_it 1.232 r_scbond_it 1.134 r_xyhbond_nbd_refined 0.397 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.232 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.183 r_chiral_restr 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1640 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 16
Software Software Software Name Purpose SAINT data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction PROTEUM PLUS data reduction SADABS data scaling XPREP data reduction Coot model building MolProbity model building