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Crystal Structure of Thioredoxin Mutant E44D 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, Ac2Cu 1 mM, 15mM Hepes pH 7.0, pH 3.5, Counter-diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.68 54.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.916 α = 90 b = 102.916 β = 90 c = 42.559 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 2005-12-23 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 51.46 99.9 0.022 29.91 21.63 12447 12447 44.395
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 0.2079 3.59 12.91 786
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 51.434 12446 12038 1180 96.761 0.234 0.234 0.228 0.2231 0.2901 0.2783 random 43.103
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] -0.759 -0.379 -0.759 1.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.034 r_dihedral_angle_3_deg 14.725 r_dihedral_angle_4_deg 12.176 r_dihedral_angle_1_deg 6.213 r_mcangle_it 1.889 r_scangle_it 1.619 r_angle_refined_deg 1.303 r_mcbond_it 1.193 r_scbond_it 1.121 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.034 r_dihedral_angle_3_deg 14.725 r_dihedral_angle_4_deg 12.176 r_dihedral_angle_1_deg 6.213 r_mcangle_it 1.889 r_scangle_it 1.619 r_angle_refined_deg 1.303 r_mcbond_it 1.193 r_scbond_it 1.121 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.221 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.187 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1627 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 24
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