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Crystal Structure of Thioredoxin Mutant D47E 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, Counterdiffusion, temperature 277K, pH 3.50
Crystal Properties Matthews coefficient Solvent content 2.69 53.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.949 α = 90 b = 102.949 β = 90 c = 41.835 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 MAR CCD 165 mm 2005-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 ESRF BM16
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 2.2 40 98.9 0.056 28.8 7.3 13367 49.98
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 2.2 2.24 97.1 0.044 3.55 6.7
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 2.2 40 12946 1281 99 0.23 0.223 0.2221 0.291 0.2829 RANDOM 35.99
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] -5.017 -2.508 -5.017 7.525
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.723 r_dihedral_angle_3_deg 16.163 r_dihedral_angle_1_deg 9.426 r_dihedral_angle_4_deg 5.47 r_scangle_it 1.926 r_angle_refined_deg 1.573 r_scbond_it 1.369 r_mcangle_it 0.75 r_mcbond_it 0.463 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.723 r_dihedral_angle_3_deg 16.163 r_dihedral_angle_1_deg 9.426 r_dihedral_angle_4_deg 5.47 r_scangle_it 1.926 r_angle_refined_deg 1.573 r_scbond_it 1.369 r_mcangle_it 0.75 r_mcbond_it 0.463 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.211 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.166 r_symmetry_hbond_refined 0.118 r_chiral_restr 0.08 r_bond_refined_d 0.013 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 1626 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 16
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction HKL-2000 data scaling Coot model building MolProbity model building