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Crystal structure of poplar glutathione transferase U20 in complex with pinocembrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8A08
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.5 277 200 mM calcium chloride, 100 mM Tris-HCl pH 8.5, 20 % w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.9 57.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.338 α = 90 b = 56.338 β = 90 c = 182.615 γ = 90
Symmetry Space Group P 41 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 100 PIXEL DECTRIS EIGER X 4M 2021-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.967700 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.6 50 100 0.062 1 28.5 27 40026 33.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 0.89 3
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 8A08 1.6 23.28 39907 1967 100 0.2145 0.2136 0.2059 0.2312 0.2198 RANDOM 33.73
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] -1.5223 -1.5223 3.0446
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.63 t_omega_torsion 3.14 t_angle_deg 0.88 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_sum_occupancies t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1731 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 28
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling MOLREP phasing