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Crystal Structure of a Genetically Modified Delta Class GST (adGSTD4-4) from Anopheles dirus, F123A, in Complex with S-Hexyl Glutathione
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F63 PDB ENTRY 3F63
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 298 30% (w/v) PEG 4000, 0.1M Sodium Cacodylate pH 6.6, 0.15M Sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 1.95 36.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.692 α = 90 b = 49.692 β = 90 c = 272.943 γ = 120
Symmetry Space Group P 32 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 ADSC QUANTUM 315 Si(111) 2006-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 30 97.6 44628 43657
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 88.1
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 (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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3F63 1.7 28.9 44628 41408 2190 97.75 0.21778 0.1745 0.17305 0.1718 0.20242 0.2013 RANDOM 25.502
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] 0.59 0.3 0.59 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.396 r_dihedral_angle_4_deg 15.652 r_dihedral_angle_3_deg 12.24 r_dihedral_angle_1_deg 5.297 r_scangle_it 2.446 r_scbond_it 1.535 r_angle_refined_deg 1.161 r_mcangle_it 0.868 r_mcbond_it 0.557 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.396 r_dihedral_angle_4_deg 15.652 r_dihedral_angle_3_deg 12.24 r_dihedral_angle_1_deg 5.297 r_scangle_it 2.446 r_scbond_it 1.535 r_angle_refined_deg 1.161 r_mcangle_it 0.868 r_mcbond_it 0.557 r_nbtor_refined 0.304 r_nbd_refined 0.189 r_symmetry_vdw_refined 0.189 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 3376 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 52
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling