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Crystal structure of monomeric Na-GST-3, a glutathione s-transferase from the major human hookworm parasite Necator americanus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ON7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 298 0.08M sodium acetate trihydrate pH 4.6, 20% (w/v) PEG 4000, 0.16M ammonium sulfate, 20% (v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.21 61.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.12 α = 90 b = 67.12 β = 90 c = 134.95 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 103.15 IMAGE PLATE RIGAKU RAXIS HTC 2013-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT
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 2.07 33.74 100 0.143 0.129 17.8 13.1 19536 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 2.07 2.24 100 0.47 0.452 0.3 12.9
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 2ON7 2.07 32.65 18561 967 99.95 0.1743 0.17191 0.1651 0.22014 0.2099 RANDOM 19.425
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] -0.34 -0.34 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.41 r_dihedral_angle_4_deg 17.842 r_dihedral_angle_3_deg 13.844 r_dihedral_angle_1_deg 5.785 r_scbond_it 3.22 r_mcangle_it 2.457 r_angle_refined_deg 2.006 r_mcbond_it 1.736 r_chiral_restr 0.151 r_bond_refined_d 0.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.41 r_dihedral_angle_4_deg 17.842 r_dihedral_angle_3_deg 13.844 r_dihedral_angle_1_deg 5.785 r_scbond_it 3.22 r_mcangle_it 2.457 r_angle_refined_deg 2.006 r_mcbond_it 1.736 r_chiral_restr 0.151 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_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 1663 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 43
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling