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Crystal Structure of Thioredoxin mutant E85D 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 3.5 277 60% (v/v) MPD, Hepes 15 mM pH 7.0, 1 mM Ac2Cu, Counter-diffusion, temperature 277K, pH 3.50
Crystal Properties Matthews coefficient Solvent content 2.63 53.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.507 α = 90 b = 103.507 β = 90 c = 41.396 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 2.25 40 99 0.059 25.82 7.1 12290 47.21
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 2.25 2.29 95.5 0.352 3.69 6.1
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 (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 40 12128 586 99.1 0.227 0.227 0.225 0.2183 0.268 0.2605 RANDOM 42.84
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] -4.981 -2.491 -4.981 7.472
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.288 r_dihedral_angle_4_deg 24.163 r_dihedral_angle_3_deg 15.364 r_dihedral_angle_1_deg 6.425 r_scangle_it 2.616 r_scbond_it 1.929 r_angle_refined_deg 1.518 r_mcangle_it 0.975 r_mcbond_it 0.537 r_xyhbond_nbd_refined 0.452
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.288 r_dihedral_angle_4_deg 24.163 r_dihedral_angle_3_deg 15.364 r_dihedral_angle_1_deg 6.425 r_scangle_it 2.616 r_scbond_it 1.929 r_angle_refined_deg 1.518 r_mcangle_it 0.975 r_mcbond_it 0.537 r_xyhbond_nbd_refined 0.452 r_nbtor_refined 0.3 r_nbd_refined 0.212 r_symmetry_hbond_refined 0.198 r_symmetry_vdw_refined 0.184 r_chiral_restr 0.091 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 80 Heterogen Atoms 24
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