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Crystal structure of the periplasmic thioredoxin SoxS from Paracoccus pantotrophus (oxidized form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other derived from SoxS MAD data
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 291 0.1M citrate, 0.4M sodium phosphate, 0.4M potassium phosphate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.4 48.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81 α = 90 b = 81 β = 90 c = 33.1 γ = 120
Symmetry Space Group P 31 2 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 CCD OXFORD ONYX CCD mirrors 2006-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OXFORD DIFFRACTION ENHANCED ULTRA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.05 12.04 99.52 0.125 0.125 36.02 33.61 8063 7981 17.26
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) 2.05 2.16 100 0.5 0.5 6.15 19.65 1152
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 derived from SoxS MAD data 2.05 12.04 7621 389 100 0.17681 0.17681 0.17476 0.173 0.21637 0.2173 RANDOM 16.424
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] 0.36 0.18 0.36 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.787 r_dihedral_angle_1_deg 19.516 r_dihedral_angle_4_deg 16.317 r_dihedral_angle_3_deg 15.425 r_scangle_it 3.264 r_scbond_it 2.048 r_angle_refined_deg 1.608 r_mcangle_it 1.497 r_mcbond_it 0.914 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.787 r_dihedral_angle_1_deg 19.516 r_dihedral_angle_4_deg 16.317 r_dihedral_angle_3_deg 15.425 r_scangle_it 3.264 r_scbond_it 2.048 r_angle_refined_deg 1.608 r_mcangle_it 1.497 r_mcbond_it 0.914 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.214 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.198 r_symmetry_hbond_refined 0.196 r_chiral_restr 0.155 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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 789 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement CrysalisPro data collection CrysalisPro data reduction SCALA data scaling MOLREP phasing