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Crystal structure of Trx domain of Grx3 from Saccharomyces cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D6I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 289.15 0.1 M Tris-HCl, pH 8.0, 2 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.01 38.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.329 α = 90 b = 77.329 β = 90 c = 37.113 γ = 90
Symmetry Space Group P 41 21 2
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 ADSC QUANTUM 315r 2016-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 1.5418 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.4 50 99.6 40 6.9 22509
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.403 1.44 96.44 0.046 0.046 2.8 6.9
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 3D6I 1.4 34.58 21310 1152 99.4 0.19004 0.18851 0.2132 0.21907 0.2325 RANDOM 20.83
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.785 r_dihedral_angle_3_deg 13.623 r_long_range_B_refined 6.278 r_long_range_B_other 6.271 r_scangle_other 5.484 r_dihedral_angle_1_deg 4.786 r_scbond_it 3.908 r_scbond_other 3.889 r_mcangle_other 2.577 r_mcangle_it 2.576
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.785 r_dihedral_angle_3_deg 13.623 r_long_range_B_refined 6.278 r_long_range_B_other 6.271 r_scangle_other 5.484 r_dihedral_angle_1_deg 4.786 r_scbond_it 3.908 r_scbond_other 3.889 r_mcangle_other 2.577 r_mcangle_it 2.576 r_angle_refined_deg 2.409 r_mcbond_it 1.884 r_mcbond_other 1.874 r_angle_other_deg 0.987 r_chiral_restr 0.134 r_bond_refined_d 0.03 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 922 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing