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Crystal structure of a Delta class GST (adGSTD4-4) from Anopheles dirus, with glutathione complexed in one subunit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JLW PDB ENTRY 1JLW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 298 0.1M Sodium Cacodylate pH 6.6, 30% (w/v) PEG 4000, 0.15M Sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.99 38.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.378 α = 90 b = 50.378 β = 90 c = 272.049 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 315r 2006-06-22 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) 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 2.05 20 98.5 0.053 36.552 9.4 26234
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.12 94.1 0.177 11.94 9.1 2451
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 ENTRY 1JLW 2.05 20 24328 1303 97.1 0.20235 0.19988 0.1976 0.24827 0.2399 RANDOM 33.992
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] 0.55 0.27 0.55 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.807 r_dihedral_angle_4_deg 19.586 r_dihedral_angle_3_deg 14.672 r_dihedral_angle_1_deg 5.493 r_scangle_it 2.437 r_scbond_it 1.57 r_angle_refined_deg 1.201 r_mcangle_it 0.992 r_mcbond_it 0.6 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.807 r_dihedral_angle_4_deg 19.586 r_dihedral_angle_3_deg 14.672 r_dihedral_angle_1_deg 5.493 r_scangle_it 2.437 r_scbond_it 1.57 r_angle_refined_deg 1.201 r_mcangle_it 0.992 r_mcbond_it 0.6 r_nbtor_refined 0.301 r_symmetry_hbond_refined 0.274 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 3297 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 20
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling