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Structural characterization of catalytic site of a Nilaparvata lugens delta-class glutathione transferase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 1M LiCl2, 30% PEG 6000, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.05 39.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.552 α = 90 b = 49.104 β = 99.9 c = 74.184 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD 2013-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 36.54 21.19 42310 27.3 3.78
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 1.73 98.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.7 36.5 40131 2125 98.5 0.17676 0.17456 0.21715 0.2309 RANDOM 23.322
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] 0.01 0.07 -0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.41 r_dihedral_angle_4_deg 28.547 r_dihedral_angle_3_deg 13.37 r_dihedral_angle_1_deg 6.014 r_long_range_B_refined 5.768 r_long_range_B_other 5.676 r_scangle_other 4.991 r_scbond_it 3.539 r_scbond_other 3.537 r_mcangle_it 3.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.41 r_dihedral_angle_4_deg 28.547 r_dihedral_angle_3_deg 13.37 r_dihedral_angle_1_deg 6.014 r_long_range_B_refined 5.768 r_long_range_B_other 5.676 r_scangle_other 4.991 r_scbond_it 3.539 r_scbond_other 3.537 r_mcangle_it 3.266 r_mcangle_other 3.266 r_mcbond_it 2.492 r_mcbond_other 2.488 r_angle_other_deg 2.279 r_angle_refined_deg 1.72 r_chiral_restr 0.114 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_gen_planes_other 0.009 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3328 Nucleic Acid Atoms Solvent Atoms 338 Heterogen Atoms 56
Software Software Software Name Purpose HKL-2000 data collection MERLOT phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling