☰ Navigation Tabs
Crystal Structure of Thioredoxin Mutant D43E 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 7 277 60% (v/v) MPD, Ac2Cu 1 mM, Hepes 15 mM pH 7.0, Counter-diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.67 54.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.991 α = 90 b = 102.991 β = 90 c = 42.445 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 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 2.45 44.6 99.9 0.0319 22.19 9.43 9672 9672 49.495
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 2.45 2.5 100 0.2322 3.93 8.26 574
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 Throuhgout pdb entry 2TRX 2.45 44.6 9672 9589 462 99.275 0.212 0.212 0.2088 0.2074 0.278 0.2644 Random 28.1
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] -3.366 -1.683 -3.366 5.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.677 r_dihedral_angle_4_deg 20.675 r_dihedral_angle_3_deg 16.752 r_dihedral_angle_1_deg 6.14 r_scangle_it 1.976 r_mcangle_it 1.929 r_angle_refined_deg 1.731 r_scbond_it 1.415 r_mcbond_it 1.265 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.677 r_dihedral_angle_4_deg 20.675 r_dihedral_angle_3_deg 16.752 r_dihedral_angle_1_deg 6.14 r_scangle_it 1.976 r_mcangle_it 1.929 r_angle_refined_deg 1.731 r_scbond_it 1.415 r_mcbond_it 1.265 r_nbtor_refined 0.313 r_nbd_refined 0.243 r_symmetry_hbond_refined 0.229 r_symmetry_vdw_refined 0.21 r_xyhbond_nbd_refined 0.195 r_chiral_restr 0.108 r_bond_refined_d 0.02 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1645 Nucleic Acid Atoms Solvent Atoms 79 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