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Glutathione Transferase-2, apo form, from the nematode Heligmosomoides polygyrus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PD2 pdb entry 1PD2 (Prostaglandin D synthase)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 292 PEG 20K, calcium chloride, Tris-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.64 41.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.678 α = 79.09 b = 74.034 β = 80.08 c = 88.573 γ = 81.55
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 210 Rh-coated Si monochromatic mirrors 2002-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.947 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.7 25 95.9 0.067 12.6 6.2 184048 184048 26.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 81.4 0.394 2 2.8 15605
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 1PD2 (Prostaglandin D synthase) 1.71 25 184047 179478 4568 95.22 0.18132 0.18002 0.1892 0.23198 0.24 RANDOM 29.053
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] -1.2 0.77 1.04 -0.8 -1.91 2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.311 r_dihedral_angle_4_deg 17.622 r_dihedral_angle_3_deg 16.876 r_dihedral_angle_1_deg 5.696 r_scangle_it 3.37 r_scbond_it 2.445 r_angle_refined_deg 1.798 r_mcangle_it 1.393 r_mcbond_it 1.095 r_angle_other_deg 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.311 r_dihedral_angle_4_deg 17.622 r_dihedral_angle_3_deg 16.876 r_dihedral_angle_1_deg 5.696 r_scangle_it 3.37 r_scbond_it 2.445 r_angle_refined_deg 1.798 r_mcangle_it 1.393 r_mcbond_it 1.095 r_angle_other_deg 1 r_mcbond_other 0.352 r_symmetry_vdw_other 0.296 r_xyhbond_nbd_refined 0.242 r_nbd_refined 0.234 r_symmetry_vdw_refined 0.226 r_symmetry_hbond_refined 0.215 r_nbd_other 0.199 r_chiral_restr 0.144 r_nbtor_other 0.093 r_xyhbond_nbd_other 0.028 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12394 Nucleic Acid Atoms Solvent Atoms 1860 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling BEAST phasing