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Crystal structure of Saccharomyces cerevisiae Gtt2 in complex with glutathione
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ERG PDB ENTRY 3ERG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 290 0.1M Tris, 2M ammoniun sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.98 58.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.774 α = 90 b = 88.774 β = 90 c = 69.102 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 IMAGE PLATE MAR scanner 345 mm plate 2009-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.1 40 99.2 0.077 0.077 15.5 4.8 18606 17631 -3
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 2.1 2.18 96.6 0.245 0.245 5.9 4.4 1778
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 ENTRY 3ERG 2.1 40 18606 17631 950 99.26 0.21002 0.20811 0.2075 0.2469 0.246 RANDOM 30.487
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] -1.51 -0.75 -1.51 2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.511 r_dihedral_angle_4_deg 16.425 r_dihedral_angle_3_deg 14.542 r_dihedral_angle_1_deg 5.32 r_scangle_it 3.123 r_scbond_it 1.938 r_angle_refined_deg 1.437 r_mcangle_it 1.26 r_mcbond_it 0.679 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.511 r_dihedral_angle_4_deg 16.425 r_dihedral_angle_3_deg 14.542 r_dihedral_angle_1_deg 5.32 r_scangle_it 3.123 r_scbond_it 1.938 r_angle_refined_deg 1.437 r_mcangle_it 1.26 r_mcbond_it 0.679 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1653 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 20
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling