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Crystal structure of the disulfide-linked complex of the thiosulfodyrolase SoxB with the carrier-protein SoxYZ from Thermus thermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WDF PDB ENTRIES 2WDF, 1V8H AND AN UNPUBLISHED SOXY STRUCTURE experimental model PDB 1V8H PDB ENTRIES 2WDF, 1V8H AND AN UNPUBLISHED SOXY STRUCTURE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.3 0.1M TRIS-HCL, 0.2M (NH4)2SO4, 8.55% PEG 8000, PH 8.3
Crystal Properties Matthews coefficient Solvent content 2.87 57.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.22 α = 86.51 b = 115.95 β = 83.21 c = 120.94 γ = 89.77
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 CCD 2012-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 3.28 59.81 98.7 0.09 7.9 2 112492 1 90.37
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 3.28 3.37 98.4 0.3 1.9 2
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Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRIES 2WDF, 1V8H AND AN UNPUBLISHED SOXY STRUCTURE 3.28 59.81 57113 2894 98.52 0.2696 0.2693 0.288 0.2747 0.2919 RANDOM 92.77
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] -24.3031 8.1134 1.4763 0.3326 6.0785 23.9704
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.51 t_omega_torsion 1.48 t_angle_deg 0.84 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.51 t_omega_torsion 1.48 t_angle_deg 0.84 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23062 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 8
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing