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Crystal Structure of Thioredoxin Mutant D9E in Hexagonal (p61) Space Group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TRX 2TRX-A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 3.5 277 60% (v/v) MPD, Ac2Cu 1 mM, Hepes 15 mM pH 7.0, Counter-diffusion, temperature 277K, pH 3.50
Crystal Properties Matthews coefficient Solvent content 2.54 51.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.026 α = 90 b = 103.026 β = 90 c = 40.279 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 2006-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER
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 2.7 40.28 99.6 0.0366 22.53 11.81 6875 58.51
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 2.7 2.8 98.9 0.3791 3.19 5.8
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 2TRX-A 2.7 40.28 6852 324 99.4 0.21 0.206 0.2005 0.292 0.2828 RANDOM 52.48
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] -4.304 -2.152 -4.304 6.456
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.735 r_dihedral_angle_4_deg 19.281 r_dihedral_angle_3_deg 17.876 r_dihedral_angle_1_deg 6.702 r_scangle_it 2.095 r_angle_refined_deg 1.619 r_scbond_it 1.251 r_mcangle_it 0.843 r_mcbond_it 0.474 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.735 r_dihedral_angle_4_deg 19.281 r_dihedral_angle_3_deg 17.876 r_dihedral_angle_1_deg 6.702 r_scangle_it 2.095 r_angle_refined_deg 1.619 r_scbond_it 1.251 r_mcangle_it 0.843 r_mcbond_it 0.474 r_nbtor_refined 0.318 r_nbd_refined 0.241 r_xyhbond_nbd_refined 0.199 r_symmetry_vdw_refined 0.197 r_symmetry_hbond_refined 0.165 r_chiral_restr 0.097 r_bond_refined_d 0.019 r_gen_planes_refined 0.005 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_refined 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 1625 Nucleic Acid Atoms Solvent Atoms 61 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