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Yeast Thiol Specific antoxidant 2 with C171S mutation and catalytic cysteine alkylated with iodoacetamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DVB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 10 % w/v PEG 6000, 5 % v/v 2-Methyl-2,4-pentanediol, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.22 44.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.365 α = 90 b = 177.306 β = 103.28 c = 115.262 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 110 PIXEL DECTRIS PILATUS 2M 2016-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.4586 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.6 47.4 97.9 0.122 0.149 0.994 6.6 2.8 62339
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.61 2.76 1.751 2.169 0.236
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 5DVB 2.6 47.4 59320 3018 97.73 0.1995 0.198 0.1941 0.2294 0.224 RANDOM 74.058
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] -8.36 16.23 -37.66 46.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39 r_dihedral_angle_4_deg 22.645 r_dihedral_angle_3_deg 19.757 r_dihedral_angle_1_deg 6.907 r_angle_refined_deg 2.264 r_angle_other_deg 1.144 r_chiral_restr 0.142 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39 r_dihedral_angle_4_deg 22.645 r_dihedral_angle_3_deg 19.757 r_dihedral_angle_1_deg 6.907 r_angle_refined_deg 2.264 r_angle_other_deg 1.144 r_chiral_restr 0.142 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12803 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms
Software Software Software Name Purpose XDS data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing