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Crystal Structure of Human Thioredoxin Mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ERT PDB ENTRY 1ERT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 289 20% PEG 3350, 0.1 M sodium acetate, 2 mM DTT, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.93 36.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.269 α = 90 b = 50.182 β = 94.08 c = 51.066 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M RH COATED FLAT MIRROR, TOROIDAL FOCUSING MIRROR 2011-01-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9796 SSRL BL9-2
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 0.97 50.94 84.2 0.042 18.8 3.4 88291 88291
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 0.97 1.02 44.5 0.316 2.6 1.6
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 (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 1ERT 0.97 35.75 83851 83851 4412 84.1 0.13726 0.13582 0.1408 0.16498 0.1709 RANDOM 14.371
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] -1.12 -1.25 1.51 -0.21
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 54.765 r_dihedral_angle_2_deg 32.9 r_sphericity_bonded 21.469 r_dihedral_angle_3_deg 14.126 r_long_range_B_refined 10.597 r_long_range_B_other 7.011 r_dihedral_angle_1_deg 6.099 r_rigid_bond_restr 5.264 r_scangle_other 2.697 r_scbond_it 2.51
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 54.765 r_dihedral_angle_2_deg 32.9 r_sphericity_bonded 21.469 r_dihedral_angle_3_deg 14.126 r_long_range_B_refined 10.597 r_long_range_B_other 7.011 r_dihedral_angle_1_deg 6.099 r_rigid_bond_restr 5.264 r_scangle_other 2.697 r_scbond_it 2.51 r_scbond_other 2.42 r_mcangle_it 2.366 r_mcangle_other 2.295 r_angle_refined_deg 1.99 r_mcbond_it 1.792 r_mcbond_other 1.789 r_angle_other_deg 1.021 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 0.003 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1634 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms
Software Software Software Name Purpose XDS data scaling MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALA data scaling