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Structure of GSTO1 covalently conjugated to quinolinic acid fluorosulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IS0 PDB 4IS0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 298 5 mg/mL solution of protein crystallized from precipitant solution containing 2.4 M ammonium sulfate and 0.1 M MES solution pH 5. Crystals cryoprotected by brief immersion in solution containing 1.5 M ammonium sulfate, 25% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.39 48.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.161 α = 90 b = 57.161 β = 90 c = 140.16 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 Osmic VariMax 2016-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rpim 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 49.5 100 0.118 0.043 0.998 11.9 8.6 18695 25.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 100 0.914 0.329 0.704 2.4 8.7
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 4IS0 2 49.5 17677 967 99.89 0.17274 0.16988 0.1781 0.22991 0.2341 RANDOM 33.638
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] 0.29 0.15 0.29 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.884 r_dihedral_angle_4_deg 20.529 r_dihedral_angle_3_deg 13.69 r_long_range_B_refined 6.674 r_long_range_B_other 6.674 r_dihedral_angle_1_deg 5.624 r_scangle_other 4.188 r_mcangle_it 2.8 r_mcangle_other 2.799 r_scbond_it 2.636
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.884 r_dihedral_angle_4_deg 20.529 r_dihedral_angle_3_deg 13.69 r_long_range_B_refined 6.674 r_long_range_B_other 6.674 r_dihedral_angle_1_deg 5.624 r_scangle_other 4.188 r_mcangle_it 2.8 r_mcangle_other 2.799 r_scbond_it 2.636 r_scbond_other 2.634 r_mcbond_other 1.78 r_mcbond_it 1.779 r_angle_refined_deg 1.385 r_angle_other_deg 0.93 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1917 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing