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Structural analysis of an epsilon-class glutathione S-transferase from housefly, Musca domestica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JLV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.2 M sodium citrate, 0.1 M HEPES-NaOH pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.91 57.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.548 α = 90 b = 87.548 β = 90 c = 131.883 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315 2009-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.8 75.8 98.3 104764 102983
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 1.8 1.9 97.4
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 1JLV 1.8 65.82 99532 97850 5130 98.31 0.16532 0.16398 0.1704 0.19052 0.1976 RANDOM 25.7
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] -0.86 -0.86 -0.86 2.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.195 r_dihedral_angle_4_deg 25.912 r_dihedral_angle_3_deg 13.801 r_dihedral_angle_1_deg 5.382 r_angle_refined_deg 1.719 r_angle_other_deg 0.983 r_chiral_restr 0.134 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.195 r_dihedral_angle_4_deg 25.912 r_dihedral_angle_3_deg 13.801 r_dihedral_angle_1_deg 5.382 r_angle_refined_deg 1.719 r_angle_other_deg 0.983 r_chiral_restr 0.134 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d 0.005 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 6986 Nucleic Acid Atoms Solvent Atoms 934 Heterogen Atoms 80
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling