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Crystal structure of the periplasmic thioredoxin SoxS from Paracoccus pantotrophus (reduced form)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 291 0.1M citrate, 0.4M sodium phosphate, 0.4M potassium phosphate, 3% (w/v) glucose, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.36 47.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.909 α = 90 b = 80.909 β = 90 c = 33.212 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 MARMOSAIC 225 mm CCD mirrors 2006-09-22 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.95369, 0.97833, 0.97838, 1.0332 EMBL/DESY, HAMBURG X12
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 1.9 20.71 99.3 0.083 0.083 30.87 6.3 10064 9998 18.37
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) 1.9 1.94 97.9 0.447 0.447 6.36 5.1 662
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 MAD THROUGHOUT 1.9 20.71 9557 9530 480 99.72 0.15668 0.15668 0.1544 0.1541 0.20124 0.2031 RANDOM 22.168
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] 0.3 0.15 0.3 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.723 r_dihedral_angle_4_deg 19.553 r_dihedral_angle_3_deg 15.954 r_dihedral_angle_1_deg 5.667 r_scangle_it 4.157 r_scbond_it 2.847 r_mcangle_it 1.738 r_mcbond_it 1.659 r_angle_refined_deg 1.512 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.723 r_dihedral_angle_4_deg 19.553 r_dihedral_angle_3_deg 15.954 r_dihedral_angle_1_deg 5.667 r_scangle_it 4.157 r_scbond_it 2.847 r_mcangle_it 1.738 r_mcbond_it 1.659 r_angle_refined_deg 1.512 r_nbtor_refined 0.32 r_nbd_refined 0.225 r_symmetry_vdw_refined 0.216 r_symmetry_hbond_refined 0.214 r_xyhbond_nbd_refined 0.192 r_chiral_restr 0.098 r_bond_refined_d 0.012 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 799 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling Auto-Rickshaw phasing